Atoms and Molecules

Everyday Science
An atom is the smallest "piece" of an element that still has the properties of that element. A molecule is a combination of two or more atoms bonded together.

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Atoms and Molecules

Table of Content

Atom and Molecules.................................................................................................. 3 Molecular science ............................................................................................... 10 Molecular geometry............................................................................................. 11 Molecular spectroscopy....................................................................................... 11

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Atom and Molecules

Atom:
An atom is the smallest "piece" of an element that still has the properties of that element. For example, an atom of gold is the smallest piece of gold that still acts like gold divide that atom any further and the particles inside are no longer gold. Atoms are much too small to see or feel with our human senses, but evidence from scientific instruments and studies clearly indicates that they are at the heart of all objects and matter in the universe. When many atoms come together, atoms tend to form molecules.

Molecule:
A molecule is a combination of two or more atoms bonded together. For example, a molecule of water (designated by the symbol H2O) consists of two hydrogen atoms and oxygen atoms which are in a "relationship" held together by an electric attraction. The basic building blocks of the "normal" matter that we see in the Universe are atoms, and combinations of atoms that we call molecules. We first consider atoms and then molecules. However, we shall see that although "normal matter" is composed of atoms and molecules, most of the matter in the Universe is not in the form of atoms or molecules, but rather in the form of a plasma. We discuss plasmas in the next section.

Constituents of Atoms
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Atoms are composed of three classes of constituents, as illustrated in the following table
. Constituent Electrons Protons Neutrons Symbol ep+ n Charge -1 +1 0 Mass 9.1 x 10-28 g 1836 x electron mass Approximately that of p+

Thus, most of the mass of atoms resides in the neutrons and protons which occupy the dense central region called the nucleus (see the Bohr atom below). The number of protons (or the number of electrons) is called the atomic number for the atom. The total number of protons plus neutrons is called the atomic mass number for the atom. Atoms are electrically neutral because the number of negatively-charged electrons is exactly equal to the number of positively-charged protons. The number of neutrons is approximately equal to the number of protons for stable light nuclei, and is about 1-2 times the number of protons for the heavier stable nuclei.

Isotopes of an Element
Atoms having the same number of protons (and therefore the same number of electrons) but different numbers of neutrons are called isotopes of the element in question. Thus, the isotopes of an element have the same atomic number but differ in their atomic mass number. A compact notation for isotopes of an element is illustrated by the following examples.

In this notation the element is represented by its chemical symbol, the atomic number is denoted by a lower left subscript, the number of neutrons is denoted by a lower right subscript, and the atomic mass number is denoted by an upper left superscript (some of these superscripts and subscripts may be omitted, depending on the context).
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Thus, the above symbols denote, respectively, the mass-235 and mass-238 isotopes of uranium (symbol U), and the mass-1,-2,and -3 isotopes of hydrogen (symbol H). The mass-2 isotope of hydrogen is also called deuterium and the mass-3 isotope is also called tritium.

The Bohr Atomic Model

The most important properties of atomic and molecular structure may be exemplified using a simplified picture of an atom that is called the Bohr Model. This model was proposed by Niels Bohr in 1915; it is not completely correct, but it has many features that are approximately correct and it is sufficient for much of our discussion. The correct theory of the atom is called quantum mechanics; the Bohr Model is an approximation to quantum mechanics that has the virtue of being much simpler.

A Planetary Model of the Atom

The Bohr Model is probably familar as the "planetary model" of the atom illustrated in the adjacent figure that, for example, is used as a symbol for atomic energy (a bit of a misnomer, since the energy in "atomic energy" is actually the energy of the nucleus, rather than the entire atom). In the Bohr Model the neutrons and protons (symbolized by red and blue balls in the adjacent image) occupy a dense central region called the nucleus, and the electrons orbit the nucleus much like planets orbiting the Sun (but the The Bohr atom orbits are not confined to a plane as is approximately true in the Solar System). The adjacent image is not to scale since in the realistic case the radius of the nucleus is about 100,000 times smaller than the radius of the entire atom, and as far as we can tell electrons are point particles without a physical extent. This similarity between a planetary model and the Bohr Model of the atom ultimately arises because the attractive gravitational force in a solar system and the attractive Coulomb (electrical) force between the positively charged nucleus
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and the negatively charged electrons in an atom are mathematically of the same form. (The form is the same, but the intrinsic strength of the Coulomb interaction is much larger than that of the gravitational interaction; in addition, there are positive and negative electrical charges so the Coulomb interaction can be either attractive or repulsive, but gravitation is always attractive in our present Universe.)

Quantized energy levels in hydrogen

But the Orbits Are Quantized

The basic feature of quantum mechanics that is incorporated in the Bohr Model and that is completely different from the analogous planetary model is that the energy of the particles in the Bohr atom is restricted to certain discrete values. One says that the energy is quantized. This means that only certain orbits with certain radii are allowed; orbits in between simply don't exist. The adjacent figure shows such quantized energy levels for the hydrogen atom. These levels are labeled by an integer n that is called a quantum number. The lowest energy state is generally termed the ground state. The states with successively more energy than the ground state are called the first excited state, the second excited state, and so on. Beyond an energy called the ionization potential the single electron of the hydrogen atom is no longer bound to the atom. Then the energy levels form a continuum. In the case of hydrogen, this continuum starts at 13.6 eV above the ground state ("eV" stands for "electron-Volt", a common unit of energy in atomic physics).

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Although this behavior may seem strange to our minds that are trained from birth by watching phenomena in the macroscopic world, this is the way things behave in the strange world of the quantum that holds sway at the atomic level.

Atomic Excitation and De-excitation

Atoms can make transitions between the orbits allowed by quantum mechanics by absorbing or emitting exactly the energy difference between the orbits. The following figure shows an atomic excitation cause by absorption of a photon and an atomic de-excitation caused by emission of a photon.

Excitation by absorption of light and de-excitation by emission of light

In each case the wavelength of the emitted or absorbed light is exactly such that the photon carries the energy difference between the two orbits. This energy may be calculated by dividing the product of the Planck constant and the speed of light hc by the wavelength of the light). Thus, an atom can absorb or emit only certain discrete wavelengths (or equivalently, frequencies or energies).
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Ionization of Atoms
Ionization is the gain or loss of electrons. The loss of electrons, which is the more common process in astrophysical environments, converts an atom into a positively charged ion, while the gain of electrons converts an atom into a negatively charged ion. In the subsequent discussion, we will use the terms ionization and ionize in the sense of losing electrons to form positive ions. There is a standard notation in astrophysics for various levels of ionization of an atom. As illustrated in the following table, this notation uses increasing Roman numerals to indicate higher levels of ionization.
Notation for Degrees of Ionization
Suffix I II III Ionization Not ionized (neutral) Singly ionized Doubly ionized Examples H I, He I H II, He II He III, O III Chemist's Notation H, He H+, He+ He++, O++

We also show the standard chemist's notation for such ions, which consists of placing a right superscript on the element symbol indicating the net electrical charge on the ion (in the neutral case the superscript "0" is usually omitted). Thus, for example, we shall speak later of "H II regions", meaning volumes of space in which the radiation from nearby hot stars has completely ionized the hydrogen.

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Chemical reactions and molecules

Molecules are compounds in which the elements are in definite, fixed ratios, as seen in Figure 12. Those atoms are held together usually by one of the three types of chemical bonds discussed above. For example: water, glucose, ATP. Mixtures are compounds with variable formulas/ratios of their components. For example: soil. Molecular formulas are an expression in the simplest whole-number terms of the composition of a substance. For example, the sugar glucose has 6 Carbons, 12 hydrogens, and 6 oxygens per repeating structural unit. The formula is written C6H12O6. Figure 12. Determination of molecular weights by addition of the weights of the atoms that make up the molecule. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates and WH Freeman used with permission .

Chemical reactions occur in nature, and some also can be performed in a laboratory setting. Chemical equations are linear representations of how these reactions occur. Combination reactions occur when two separate reactants are bonded together, e.g. A + B -----> AB. Disassociation reactions occur when a compound is broken into two products, e.g. AB -----> A + B.
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The combustion of propane with oxygen, resulting in carbon dioxide, water, and energy (as heat and light). This chemical reaction takes place in a camping stove as well as in certain welding torches. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates and WH Freeman used with permission.

Biological systems, while unique to each species, are based on the chemical bonding properties of carbon. Major organic chemicals (those associated with or formed by the actions of living things) usually include some ratios of the following elements: C, H, N, O, P, S.

Molecular science
The science of molecules is called molecular chemistry or molecular physics, depending on the focus. Molecular chemistry deals with the laws governing the interaction between molecules that result in the formation and breakage of chemical bonds, while molecular physics deals with the laws governing their structure and properties. In practice, however, this distinction is vague. In molecular sciences, a molecule consists of a stable system (bound state) comprising two or more atoms. Polyatomic ions may sometimes be usefully thought of as electrically charged molecules. The term unstable molecule is used for very reactive species, i.e., short-lived assemblies (resonances) of electrons and nuclei, such as radicals, molecular ions, Rydberg molecules, transition states, van
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der Waals complexes, or systems of colliding atoms as in Bose-Einstein condensate.

Molecular size
Most molecules are far too small to be seen with the naked eye, but there are exceptions. DNA, a macromolecule, can reach macroscopic sizes, as can molecules of many polymers. The smallest molecule is the diatomic hydrogen (H2), with a length of 0.74 . Molecules commonly used as building blocks for organic synthesis have a dimension of a few to several dozen . Single molecules cannot usually be observed by light (as noted above), but small molecules and even the outlines of individual atoms may be traced in some circumstances by use of an atomic force microscope. Some of the largest molecules are macromolecules or super-molecules.

Molecular geometry
Molecules have fixed equilibrium geometriesbond lengths and angles about which they continuously oscillate through vibrational and rotational motions. A pure substance is composed of molecules with the same average geometrical structure. The chemical formula and the structure of a molecule are the two important factors that determine its properties, particularly its reactivity. Isomers share a chemical formula but normally have very different properties because of their different structures. Stereoisomers, a particular type of isomers, may have very similar physico-chemical properties and at the same time different biochemical activities.

Molecular spectroscopy
Molecular spectroscopy deals with the response (spectrum) of molecules interacting with probing signals of known energy (or frequency, according to Planck's formula). Molecules have quantized energy levels that can be analyzed by detecting the molecule's energy exchange through absorbance or emission. Spectroscopy does not generally refer to diffraction studies where particles such as neutrons, electrons, or high energy X-rays interact with a regular arrangement of molecules (as in a crystal).
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Molecular Orbitals
There is a second major theory of chemical bonding whose basic ideas are distinct from those employed in valence bond theory. This alternative approach to the study of the electronic structure of molecules is called molecular orbital theory. The theory applies the orbital concept, which was found to provide the key to the understanding of the electronic structure of atoms, to molecular systems. The concept of an orbital, whether it is applied to the study of electrons in atoms or molecules, reduces a many-body problem to the same number of one-body problems. In essence an orbital is the quantum mechanical description (wave function) of the motion of a single electron moving in the average potential field of the nuclei and of the other electrons which are present in the system. An orbital theory is an approximation because it replaces the instantaneous repulsions between the electrons by some average value. The difficulty in obtaining an accurate description of an orbital is the difficulty in determining the average potential field of the other electrons. For example, the 2s orbital in the lithium atom is a function which determines the motion of an electron in the potential field of the nucleus and in the average field of the two electrons in the 1s orbital. However, the 1s orbital is itself determined by the nuclear potential field and by the average potential field exerted by the electron in the 2s orbital. Each orbital is dependent upon and determined by all the other orbitals of the system. To know the form of one orbital we must know the forms of all of them. This problem has a mathematical solution; the exploitation of this solution has proved to be one of the most powerful and widely used methods to obtain information on the electronic structure of matter. A molecular orbital differs from the atomic case only in that the orbital must describe the motion of an electron in the field of more than one nucleus, as well as in the average field of the other electrons. A molecular orbital will in general, therefore, encompass all the nuclei in the molecule, rather than being centred on a single nucleus as in the atomic case. Once the forms and properties of the molecular orbitals are known, the electronic configuration and properties of the molecule are again determined by assigning electrons to the molecular orbitals in the order of increasing energy and in accordance with the Pauli Exclusion Principle.

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In valence bond theory, a single electron pair bond between two atoms is described in terms of the overlap of atomic orbitals (or in the mathematical formulation of the theory, the product of atomic orbitals) which are centred on the nuclei joined by the bond. In molecular orbital theory the bond is described in terms of a single orbital which is determined by the field of both nuclei. The two theories provide only a first approximation to the chemical bond.

The Molecules!
Here are just a few samples of molecules.

Acetaminophen Sold as TylenolTM, this has a similar shape to another pain-killer, aspirin. They both act in a similar way to reduce pain and fever. It is comprised of: C8H9O2N 8 black carbon atoms 9 white hydrogen atoms 2 red oxygen atoms 1 blue nitrogen atom Aspirin Chemists learned to make aspirin by studying a similar pain-killing molecule discovered in willow trees. C9H8O4 9 black carbon atoms 8 white hydrogen atoms 4 red oxygen atoms

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Aspartame Sold as Nutrasweet,TM aspartame is an artificial sweetener used in sodas. It tastes a hundred times sweeter than sucrose and contains no calories. C14H18O5N2 14 black carbon atoms 18 white hydrogen atoms 5 red oxygen atoms 2 blue nitrogen atoms

Carbon Dioxide Less than 1% of the air is carbon dioxide, but it is essential for life. Plants use carbon dioxide to build energy-rich molecules. CO2 1 black carbon atom 2 red oxygen atoms

Nicotine Nicotine is in cigarette tobacco. It interacts with receptors in our brain and activates nerve cells. It is addictive and a poison. C10H14N2 10 black carbon atoms 14 white hydrogen atoms 2 blue nitrogen atoms

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Serotonin Serotonin is one of many molecules our brain cells use to pass information to each other. It regulates our moods and sleep patterns. C10H12ON2 10 black carbon atoms 12 white hydrogen atoms 1 red oxygen atom 2 blue nitrogen atoms Silk Spiders and silkmoths make silk for their webs and cocoons. Silk threads are stored in a silk gland, and dry and harden as they are spun. C10H18O5N4 10 black carbon atoms 18 white hydrogen atoms 5 red oxygen atoms 4 blue nitrogen atoms Trimethylamine Trimethylamine makes some things stink. Rotten fish, and sometimes dogs, smell bad because of this molecule. C3H9N 3 black carbon atoms 9 white hydrogen atoms 1 blue nitrogen atom

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References

http://www.nyhallsci.org/marvelousmolecules/marveloussub.html

^ a b IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (1994) "molecule". ^ Pauling, Linus (1970). General Chemistry. New York: Dover Publications, Inc.. ISBN 0486-65622-5. ^ Ebbin, Darrell, D. (1990). General Chemistry, 3rd Ed.. Boston: Houghton Mifflin Co.. ISBN 0-395-43302-9. ^ Brown, T.L. (2003). Chemistry the Central Science, 9th Ed.. New Jersey: Prentice Hall. ISBN 0-13-066997-0. ^ Chang, Raymond (1998). Chemistry, 6th Ed.. New York: McGraw Hill. ISBN 0-07115221-0. ^ Zumdahl, Steven S. (1997). Chemistry, 4th ed.. Boston: Houghton Mifflin. ISBN 0-66941794-7. ^ Chandra, Sulekh. Comprehensive Inorganic Chemistry. New Age Publishers. ISBN 8122415121. ^ Molecule, Encyclopaedia Britannica on-line ^ Molecule Definition (Frostburg State University) ^ Roger L. DeKock, Harry B. Gray (1989). Chemical structure and bonding. University Science Books. p. 199. ISBN 093570261X. ^ Chang RL, Deen WM, Robertson CR, Brenner BM. (1975). "Permselectivity of the glomerular capillary wall: III. Restricted transport of polyanions". Kidney Int. 8 (4): 212218. doi:10.1038/ki.1975.104. PMID 1202253. ^ a b Ponomarev 1993, pp. 1415. ^ McEvilley 2002, p. 317. ^ King 1999, pp. 105107. ^ Moran 2005, p. 146. ^ a b Levere 2001, p. 7. ^ Pratt, Vernon (September 28, 2007). "The Mechanical Philosophy". Reason, nature and the human being in the West. Retrieved 2009-06-28. ^ Siegfried 2002, pp. 4255. ^ Kemerling, Garth (August 8, 2002). "Corpuscularianism". Philosophical Dictionary. Retrieved 2009-06-17. ^ "Lavoisier's Elements of Chemistry". Elements and Atoms. Le Moyne College, Department of Chemistry. Retrieved 2007-12-18. ^ Wurtz 1881, pp. 12. ^ Dalton 1808. ^ Roscoe 1895, pp. 129. ^ Einstein, Albert (1905). "ber die von der molekularkinetischen Theorie der Wrme geforderte Bewegung von in ruhenden Flssigkeiten suspendierten Teilchen" (in German)
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(PDF). Annalen der Physik 322 (8): 549560. Bibcode 1905AnP...322..549E. doi:10.1002/andp.19053220806. Retrieved 2007-02-04. ^ Mazo 2002, pp. 17. ^ Lee, Y.K.; Hoon, K. (1995). "Brownian Motion". Imperial College. Retrieved 2007-1218. ^ Patterson, G. (2007). "Jean Perrin and the triumph of the atomic doctrine". Endeavour 31 (2): 5053. doi:10.1016/j.endeavour.2007.05.003. PMID 17602746. ^ "Periodic Table of the Elements". The International Union of Pure and Applied Chemistry. November 1, 2007. Retrieved 2010-05-14. ^ Scerri 2007, pp. 1017. ^ "J.J. Thomson". Nobel Foundation. 1906. Retrieved 2007-12-20. ^ Rutherford, E. (1911). "The Scattering of and Particles by Matter and the Structure of the Atom". Philosophical Magazine 21: 66988.

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