Ochiai E. Chemicals for Life and Living

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21 Are Atoms and Molecules for Real? Can We See Them?

Fig. 21.2 An electronmicro-

gram of DNA molecules

Fig. 21.3

HRTEM image

of potassium iodide (K)

embedded in a carbon

nanotube. As the inset

indicates, the atoms of K

and

−

are clearly seen as separate

balls (from R. R. Myer et al.,

Science, 289 (2000),

1324–1327)

Fig. 21.4 HRTEM image of

strontium titanate (SrTiO

);

atoms of Sr, Ti, and O are

seen as separate balls (from

Z. Zhang et al., Science,

302 (2003), 846–849)

26321.2 Scanning Probe Microscopy

21.2 Scanning Probe Microscopy

Figures 21.2–21.4 illustrates the best you can do with the electron microscope.

In 1980s, two scientists, Heinrich Rohrer and Gerd Binnig at IBM’s Zürich Research

Center in Switzerland developed a revolutionary method of microscopy. They were

awarded a Nobel prize in 1986 for this invention. The principle is simple, though

technologies required to realize them are quite advanced.

Figure 21.5 illustrates the principle of scanning tunneling microscope [STM,

a kind of scanning probe microscopy (SPM)]. The probe tip is sharpened so that it

is made of a single metallic atom (to make such a probe is not an easy task). A solid

sample (a metal or a semiconductor) is placed ﬂat and the probe tip is brought very

close to the surface of the sample. If the probe comes within a few atomic distance

from the atom just below (of the sample), a strange thing happens. Electrons jump

over that distance from the atom of the probe to that of the sample. This phenome-

non is known as “tunneling” (of electron). This corresponds to a ﬂow of electric

current between the probe and the sample, though they are not in contact. It is

known that the electric current ﬂow due to tunneling is dependent on the distance

and the nature of atoms of probe and sample.

The probe is scanned across the surface of the sample, and the height of the probe

is adjusted so that the tunneling current ﬂow is kept constant as it is being scanned,

and the height can then be recorded as the probe is scanned all over the surface of

sample. This movement of the probe must necessarily be minute and precise and is

accomplished by a devise based on piezoelectricity. The trace of height of the probe

may represent the shape and arrangement of atoms and vacancies in between. The

scanning result can then be treated by a computer and be visualized.

Such an example as shown in Fig. 21.6 then can be regarded as that of the

atomic arrangement on the surface. This is gallium arsenide (GaAs); the blue rep-

resents arsenic atoms and the red gallium. Each hump represents a single atom.

This is the way chemists had pictured the structure of this compound (and others)

long before a devise like STM gave them the picture of atoms in a substance.

In other words, the chemists’ depiction of atoms and molecules was not very bad.

Piezoelectric

control

Probe

Sample

Tunneling current

Feedback

generator

Reference

signal

Display

Fig. 21.5 A schematic

presentation of STM

264

21 Are Atoms and Molecules for Real? Can We See Them?

By the way, gallium arsenide is expected to function as a semiconductor like

silicon, which is the basis of the today’s high-technology industry. The diameters

of gallium and arsenide can then be estimated from this result. They are about 0.2

and 0.4 nm (2 and 4 Å), respectively, and are in agreement with the data obtained

by other methods. These results suggest that the resolution of STM is of the order

of 0.01 nm (=0.1 Å = 10 pm).

Astonishingly, a small molecule like dioxygen O

, which is the form of oxygen

found in the air, has also been imaged by STM. Figure 21.7 shows two O

molecules

bound (adsorbed) on the surface of silicon. The extra blob just above the oxygen

molecule at the left-hand corner is a defect in the underlying silicon crystal. As you

see, the dioxygen molecule looks like a dumbbell; i.e., each dioxygen molecule is

made of two spheres bound together. These molecules do not look like being bound

ﬂat to the surface, but being bound slanted. The sphere that represents an atom is

actually the shape of the electron cloud around the nucleus. Again this is the same

as the picture chemists have been using to represent the oxygen molecule O–O.

Figure 21.8 gives an STM image of benzene molecule adsorbed on a rhodium metal

surface. The positions of six carbon atoms and six hydrogen atoms are shown by

Fig. 21.7 STM image of

dioxygen molecule (from B. C.

Stipe et al., Science, 279

(1998), 1907–1909)

Fig. 21.6

STM image of

gallium arsenide (GaAs) (from

D. P. Kern et al., Science, 241

(1988), 936–944)

26521.2 Scanning Probe Microscopy

small dots in the inset portion. Because it is adsorbed on a metal, it is slightly dis-

torted from the free benzene molecule. However, the overall picture corresponds

well to the structure that chemists have been imagining based on the theories.

STM is but an example of scanning probe microscopes. Another important scan-

ning probe microscope is called atomic force microscope (AFM). When a probe is

brought close to a sample, a force will be exerted between the probe and the sample.

If this force (atomic force) is of a general character, i.e., London dispersion force,

then the force will be dependent on the distance and the nature of the probe and the

atomic nature of the sample. Hence, a geometrical structure of a sample will be

imaged at atomic level by scanning such a probe that responds to atomic force.

The double helix structure of a DNA has been imaged by AFM. That is shown in

Fig. 21.9. A DNA molecule looks like a right-handedly wound ropes. The ropes are

the (alpha) helically coiled double strand. These images (Figs. 21.6–21.9) give us

Fig. 21.8 STM image of

benzene molecule (from P.

Saulet and C. Joachim, Chem.

Phys. Lett., 185 (1991), 23)

Fig. 21.9 AFM image of DNA (from J. Mou et al., FEBS Lett., 371 (1995), 279–282)

266

21 Are Atoms and Molecules for Real? Can We See Them?

very good pictures of molecules with atomic level resolution in some cases, and

really convince us that, yes, atoms and molecules do exist, and moreover, that they

do look like how chemists have been saying they do. What more do you need to be

convinced?

21.3 X-Ray Diffraction: Atomic Structure of Large Molecular

Compounds and Ionic Compounds

The scanning probe microscopes are still unable to resolve atomic structures of such

complicated large molecules as proteins and DNAs. The atomic structures of these

large molecules (as well as smaller molecules and ionic compounds) are now almost

routinely determined by X-ray crystallography. This technique is much older than

SPM. However, the way this technique produces the atomic structure of a molecule is

not as straightforward as electron microscopy or scanning probe microscopy. Yet, the

structures obtained by this techniques, particularly those of smaller molecules and ionic

compounds, have well been veriﬁed by many other methods and experience. Therefore,

the atomic structure of a large molecule obtained by this method is also now well

believed to represent the correct structure of the compound. It is true, though, that the

structure is valid only for the solid crystal state to which this method is applied.

We will explain very brieﬂy how it is done with a few examples. X-ray is a light

of very short wavelength. For example, when an electron beam is directed to a copper

metal, the copper metal produces an X-ray of 154 pm (1.54 Å). This is the source of

light (X-ray, that is). The light (any light) shone on a compound will be scattered by

the electron clouds (of atoms) of the compound. When the atoms are arranged regu-

larly as in a crystal, this scattered light will show a pattern. This is called diffraction

pattern, and is related to the crystal structure. The diffraction pattern can be photo-

graphed or now digitally recorded. The pattern consists of spots (where the diffracted

X-ray hits) of differing intensities. The intensity of a spot is related to the electron

cloud density that scatters X-ray. (The more dense electron cloud scatters X-ray more

strongly; thus the spot will be more intense). Therefore, we can reconstruct how the

electron clouds are distributed throughout space (in a crystal) by analyzing the dif-

fraction pattern including intensities. The result can be expressed as an electron den-

sity map (in three dimensions), and that can then be reinterpreted as an aggregate of

atoms. Softwares have now been developed to convert the diffraction pattern to the

atomic arrangements in a molecule. The resolution obtained is now routinely about

1.5–2 Å (150–200 pm = 0.15–0.2 nm). Hence, we can distinguish atoms in molecules,

as the inter-atomic distances in molecules are around 1–2 Å (0.1–0.2 nm).

The actual process is now fairly automated, but one of the basic problems is to

obtain a single crystal of an appropriate size. Many biologically interesting samples

such as proteins and DNAs are difﬁcult to crystallize, and researchers would spend

days, months, and even years to get single crystals suitable for X-ray crystallographic

studies. Many other problems prevent X-ray studies of crystal structures from becom-

ing a truly routine technique. But it is not appropriate to pursue this issue further here.

Below we display a few protein structures (Figs. 21.10–21.12) determined by

X-ray crystallography. Figure 21.10 shows three different modes of expressing

267

21.3 X-Ray Diffraction: Atomic Structure of Large Molecular Compounds…

a protein structure. Mode (a) is called “ball-and-stick” representation, and uses colored

dots to indicate the position of an atom where different colors represent different ele-

ments, and the bonds are shown as sticks. In mode (b) a helical strip tape is used to

schematically represent a helical structure and a string is a random coil portion.

Another major secondary structure is b-strand, and it is represented by ﬂattened tape

as seen in Fig. 21.11. In mode (c), amino acids of different characters are represented

by colored balls; in this case yellow: hydrophobic amino acid, blue: hydrophilic

(electrically charged) amino acid and white: others. An account of the protein struc-

ture, including the secondary structures a-helix and b-strand, is found in Fig. 5.4.

Fig. 21.10 Structures of myoglobin as determined by X-ray crystallography; myoglobin is the

oxygen-binding protein in muscle. (a) shows all the atoms except for hydrogen as small balls;

(b) ribbon presentation of secondary structure – the spiral is helix; (c) space-ﬁlling representation

of constituting amino acids (from J. M. Berg, J. L. Tymoczko and L. Stryer, “Biochemistry 5th ed”

(W. H. Freeman and Co, 2002))

Fig. 21.11

HIV-protease that consists mostly of b-strand (from J. M. Berg, J. L. Tymoczko

and L. Stryer, “Biochemistry 5th ed” (W. H. Freeman and Co, 2002))

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21 Are Atoms and Molecules for Real? Can We See Them?

HIV-protease (Fig. 21.11) is the target of one kind of AIDS drugs, as discussed

in Chap. 17. Figure 21.12 is nitrogenase, one of the most complex enzymes, and is

talked about in Chap. 6. Determination of protein (enzyme) structures as illustrated

here and others help enormously in understanding their functions and the mecha-

nisms in which they play crucial roles.

Fig. 21.12 Nitrogenase; its active sites P-cluster and FeMo cofactor are shown schematically (from

J. M. Berg, J. L. Tymoczko and L. Stryer, “Biochemistry 5th ed” (W. H. Freeman and Co, 2002))

Part VII

Postscript

271

E. Ochiai, Chemicals for Life and Living,

The readers have hopefully been convinced by now that our material world is indeed

made of chemicals, and that our entire universe, including us human beings, would

not exist without chemicals. Chemistry as a scientiﬁc discipline has been fairly well

advanced to give us a nice consistent picture of the material world. But this is a

chemical view of the world; i.e., the world is viewed only through “chemistry” eye-

glasses and in terms of chemical concepts and theories advanced so far.

Chemistry as a discipline is an analytical (reductionist) endeavor; i.e., it tries to

understand things by dissecting them into compounds (molecules and ionic ensem-

bles) and then taking account of interactions among atoms, ions, and molecules.

The reality of the world consists of a whole set of these compounds interacting with

each other in diverse ways. Compounds and molecules involved may or may not

have been known to chemistry (i.e., Homo sapiens), and chemistry may or may not

have fully recognized or understood the diverse ways they interact. In other words,

we should recognize that chemical understanding of the world as practiced by

today’s chemists is far from perfect, both in the analytical sense (i.e., we do not yet

know all the compounds existent or emerging in the whole universe and all their

interactions) and also the“synthetic” sense. Well, language here is inadequate

because chemical synthesis as a technique is widely practiced by chemists, but

“synthesis” as a philosophical concept is alien to the discipline of chemistry.

In other words, chemistry may not concern itself with synthetic understanding of

things taking into account all the material presents (known and unknown) and all the

interactions at chemical, physical, biological, and (maybe geological) levels.

This kind of limitation exists implicitly in all the so-called disciplinary sciences

or modern (western) science, but particularly acute in chemical science (and also in

many of the so-called “social science” disciplines including economics and political

sciences). The entirety of a phenomenon (material world, society, world economy,

etc.) is there as a whole, but each disciplinary science dissects it and recognizes only

an aspect (or portion) of the whole. Understanding of the world then requires more

than disciplinary understandings, and technology based on disciplinary thinking has

its limitation.

Holistic Chemical View of the World