2.2: Atoms and Basic Chemistry

The difference between elements and atoms is often confused in casual conversation. Both terms describe matter, substances with mass. Different elements are different kinds of matter distinguished by different physical and chemical properties. In turn, the atom is the fundamental unit of matter—that is, of an element. The positively charged protons and neutral neutrons in an atomic nucleus account for most of the mass of an atom. Each negatively charged electron that orbits a nucleus is about 1/2000 of the mass of a proton or neutron. Thus, they do not add much to the mass of an atom.

Electrons stay in atomic orbits because of electromagnetic forces, (i.e., their attraction to the positively charged nuclei). Nuclear size (mass) and the cloud of electrons around its nucleus define structure of an atom, and that structure dictates the different properties of the elements. Let’s take a closer look at the elements and their atoms and how their atomic properties account for the formation of molecules and molecular structure.

2.2.1. Overview of Elements and Atoms

We model atoms to illustrate the average physical location of electrons (the orbital model ) on one hand and their potential energy levels (the Bohr or shell model ) on the other (Figure 2.1).

Figure 2.1: The Bohr(shell)model of an atom (above) emphasizes electron kinetic energy; the orbital model (below) emphasizes the space occupied by electrons moving around the atomic nucleus.

Up to two electrons move in a space defined as an orbital. In addition to occupying different areas around the nucleus, electrons exist at different energy levels and move with different kinetic energy. As we will learn, electrons can absorb or lose energy, jumping or falling from one energy level to another.

Recall that atoms are chemically most stable when they are electrically uncharged, with an equal number of protons and electrons. Isotopes of the same element are atoms with the same number of protons and electrons but a different number of neutrons and thus, different masses. Isotopes of an element are chemically stable but may not be physically stable. For example, the most abundant isotope of hydrogen contains one proton, one electron, and no neutrons. The nucleus of the deuterium isotope of hydrogen contains one neutron, and that of tritium contains two neutrons. Both isotopes can be found in water molecules. Deuterium is stable. In contrast, the tritium atom is radioactive, subject to nuclear decay over time. Whether they are physically stable or not, all isotopes of an element share the same electromagnetic and chemical properties and behave the same way in chemical reactions. The electromagnetic forces that keep electrons orbiting their nuclei allow the formation of chemical bonds in molecules.

The partial periodic table below (Figure2.2) shows the elements that are essential for all life(in greater or lesser amounts), as well as some that may also be essential in humans.

Figure 2.2: Partial Periodic Table of Elements emphasizing elements found in living things

The table shows the unique atomic number (number of protons) and atomic mass (usually measured in daltons, or Da) that characterize the different elements. For example, the atomic number of carbon (C) is 6, which is the number of protons in its nucleus. Its mass is 12 Da (six protons plus six neutrons, at 1 Da each). Remember that the mass of all the electrons in a C atom is negligible! Find the C atom and look at some of the other atoms of elements in the partial periodic table (Figure2.2). Superscripted atomic numbers and subscripted atomic mass numbers uniquely define each element.

122-2 Atoms & Elements

CHALLENGE

The periodic table shows the most abundant isotope of hydrogen. What are the masses of the 3 common isotopes of hydrogen?

2.2.2. Electron Configuration - Shells and Subshells

The Bohr model of the atom reveals how electrons can absorb and release energy. The shells indicate the energy levels of electrons. Electrons can absorb different kinds of energy, including electrical energy, radiation, and light (which is just a form of radiation—weaker than some and stronger than others).

CHALLEGE

What are some stronger forms of radiation, and what makes them stronger?

Ultraviolet (UV) light beamed at atoms can excite electrons. If an electron in an atom absorbs a full quantum (a photon) of UV radiant energy, it will be boosted from the ground state (the shell it normally occupies) into a higher shell, an excited state. Excited electrons move at greater speed around the nucleus and with more kinetic energy than they did at ground state. Excited electrons also have more potential energy than ground-state electrons. This is because they are unstable, releasing some of the energy gained during excitation as they return to ground (i.e., their starting energy level, or shell, as seen below in Figure2.3).

Electrons falling back to ground typically release excitation energy as heat. Atoms whose excited electrons release their energy as light fluoresce; we say they are fluorescent. A fluorescent light is an example of this phenomenon. Electrical energy excites electrons out of their atomic orbitals in the molecules that coat the interior surface of the bulb. As all those excited electrons return to ground state, they fluoresce, releasing light. These atoms can be repeatedly excited by electricity.

As we shall see, biologists and chemists have turned fluorescence into a tool of biochemistry, molecular biology, and microscopy. The ground state is also called the resting state, but electrons at ground are by no means resting! They just move with less kinetic energy than excited electrons.

Figure 2.3: When an electron absorbs e.g., light energy, it moves faster. Absorbance of one photon causes an electron to jump to a shell farther from the atomic nucleus. While having higher kinetic energy, excited electrons are unstable. Thus, they have potential energy, which is released as the electron returns to ground state, releasing heat or light (fluorescence).

123 Electron Energy and Fluorescence