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Atomic Structure

As you probably know from your general chemistry course, an atom consists of a dense, positively charged nucleus surrounded at a relatively large dis- tance by negatively charged electrons (Figure 1.2). The nucleus consists of subatomic particles called neutrons, which are electrically neutral, and pro- tons, which are positively charged. Because an atom is neutral overall, the number of positive protons in the nucleus and the number of negative elec- trons surrounding the nucleus are the same.

Although extremely small—about 10-14 to 10-15 meter (m) in diameter the nucleus nevertheless contains essentially all the mass of the atom. Elec- trons have negligible mass and circulate around the nucleus at a distance of approximately  10-10  m. Thus, the  diameter  of  a  typical  atom  is  about 2 × 10—10 m, or 200 picometers (pm), where 1 pm = 10—12 m. To give you an idea of how small this is, a thin pencil line is about 3 million carbon atoms wide. Many organic chemists and biochemists still use the unit angstrom (Å) to express atomic distances.


schematic view of an atom. The dense, positively charged nucleus contains

Figure 1.2 A schematic view of an atom. The dense, positively charged nucleus contains most of the atom’s mass and is surrounded by nega- tively charged electrons. The three- dimensional view on the right shows calculated electron-density surfaces. Electron density increases steadily toward the nucleus and is 40 times greater at the blue solid surface than at the gray mesh surface.


A specific atom is described by its atomic number (Z), which gives the num- ber of protons (or electrons) it contains, and its mass number (A), which gives the total number of protons plus neutrons in its nucleus. All the atoms of a given element have the same atomic number—1 for hydrogen, 6 for carbon, 15 for phosphorus, and so on—but they can have different mass numbers depending on how many neutrons they contain. Atoms with the same atomic number but different mass numbers are called isotopes.


The weighted average mass in atomic mass units (amu) of an element’s naturally occurring isotopes is called the element’s atomic mass (or atomic weight)—1.008 amu for hydrogen, 12.011 amu for carbon, 30.974 amu for phosphorus, and so on.


What about the electrons? How are they distributed in an atom? According to the quantum mechanical model of atomic structure, the behavior of a specific electron in an atom can be described by a mathematical expression called a wave equation—the same sort of expression used to describe the motion of waves in a fluid. The solution to a wave equation is a wave function, or orbital, denoted by the Greek letter psi, . An orbital can be thought of as defining a region of space around the nucleus where the electron can most likely be found


What do orbitals look like? There are four different kinds of orbitals, denoted s, p, d, and f, each with a different shape. Of the four, we’ll be con- cerned only with s and p orbitals because these are the most common in organic and biological chemistry. An s orbital is spherical, with the nucleus at its center, while a p orbital is dumbbell-shaped and can be oriented in space along any of three mutually perpendicular directions, arbitrarily denoted px, py, and pz (Figure 1.3). The two parts, or lobes, of a p orbital have different algebraic signs (+ and —) in the wave function and are separated by a region of zero electron density called a node.


Representations of s and p orbitals. An s orbital  is spherical, while a p orbital is

Figure 1.3 Representations of s and p orbitals. An s orbital  is spherical, while a p orbital is dumbbell-shaped and can be oriented along any of three mutually perpendicular direc- tions. Each p orbital has two lobes separated by a node. The two lobes have different alge- braic signs in the correspond- ing wave function, as indicated by the different colors.



Orbitals are organized into different layers around the nucleus of succes- sively larger size and energy. Different layers, or electron shells, contain dif- ferent numbers and kinds of orbitals, and each orbital can be occupied by 2 electrons. The first shell contains only a single s orbital, denoted 1s, and thus holds only 2 electrons. The second shell contains an s orbital (designated 2s) and three mutually perpendicular p orbitals (each designated 2p) and thus holds a total of 8 electrons. The third shell contains an s orbital (3s), three p orbitals (3p), and five d orbitals (3d), for a total capacity of 18 electrons. These orbital groupings are shown in Figure 1.4.


The energy levels of elec- trons in an atom

Figure 1.4 The energy levels of elec- trons in an atom. The first shell holds a maximum of 2 electrons in one 1s orbital; the second shell holds a maximum of 8 electrons in one 2s and three 2p orbit- als; the third shell holds a maximum of 18 electrons in one 3s, three 3p, and five 3d orbitals; and so on. The 2 electrons in each orbital are represented by up and down arrows, hg. Although not shown, the energy level of the 4s orbital falls between 3p and 3d.