Molecular Dynamics - How it works
The physical world is made up of matter, physical substance that has mass; occupies space; is composed of atoms; and is, ultimately, convertible to energy. On Earth, three principal phases of matter exist, namely solid, liquid, and gas. The differences between these three are, on the surface at least, easily perceivable. Clearly, water is a liquid, just as ice is a solid and steam a gas. Yet, the ways in which various substances convert between phases are often complex, as are the interrelations between these phases. Ultimately, understanding of the phases depends on an awareness of what takes place at the molecular level.
An atom is the smallest particle of a chemical element. It is not, however, the smallest thing in the universe; atoms are composed of subatomic particles, including protons, neutrons, and electrons. These subatomic particles are discussed in the context of the structure of matter elsewhere in this volume, where they are examined largely with regard to their electromagnetic properties. In the present context, the concern is primarily with the properties of atomic and molecular particles, in terms of mechanics, the study of bodies in motion, and thermodynamics.
An atom must, by definition, represent one and only one chemical element, of which 109 have been identified and named. It should be noted that the number of elements changes with continuing research, and that many of the elements, particularly those discovered relatively recently—as, for instance, meitnerium (No. 109), isolated in the 1990s—are hardly part of everyday experience. So, perhaps 100 would be a better approximation; in any case, consider the multitude of possible ways in which the elements can be combined.
Musicians have only seven tones at their disposal, and artists only seven colors—yet they manage to create a seemingly infinite variety of mutations in sound and sight, respectively. There are only 10 digits in the numerical system that has prevailed throughout the West since the late Middle Ages, yet it is possible to use that system to create such a range of numbers that all the books in all the libraries in the world could not contain them. This gives some idea of the range of combinations available using the hundred-odd chemical elements nature has provided—in other words, the number of possible molecular combinations that exist in the universe.
THE STRUCTURE OF MOLECULES.
A molecule is a group of atoms joined in a single structure. Often, these atoms come from different elements, in which case the molecule represents a particular chemical compound, such as water, carbon dioxide, sodium chloride (salt), and so on. On the other hand, a molecule may consist only of one type of atom: oxygen molecules, for instance, are formed by the joining of two oxygen atoms.
As much as scientists understand about molecules and their structure, there is much that they do not know. Molecules of water are fairly easy to understand, because they have a simple, regular structure that does not change. A water molecule is composed of one oxygen atom joined by two hydrogen atoms, and since the oxygen atom is much larger than the two hydrogens, its shape can be compared to a basketball with two softballs attached. The scale of the molecule, of course, is so small as to boggle the mind: to borrow an illustration from American physicist Richard Feynman (1918-1988), if a basketball were blown up to the size of Earth, the molecules inside of it would not even be as large as an ordinary-sized basketball.
As for the water molecule, scientists know a number of things about it: the distance between the two hydrogen atoms (measured in units called an angstrom), and even the angle at which they join the oxygen atom. In the case of salt, however, the molecular structure is not nearly as uniform as that of water: atoms join together, but not always in regular ways. And then there are compounds far more complex than water or salt, involving numerous elements that fit together in precise and complicated ways. But, once that discussion is opened, one has stepped from the realm of physics into that of chemistry, and that is not the intention here. Rather, the purpose of the foregoing and very cursory discussion of molecular structure is to point out that molecules are at the heart of all physical existence—and that the things we cannot see are every bit as complicated as those we can.
Given the tiny—to use an understatement—size of molecules, how do scientists analyze their behavior? Today, physicists have at their disposal electron microscopes and other advanced forms of equipment that make it possible to observe activity at the atomic and molecular levels. The technology that makes this possible is beyond the scope of the present discussion.
Obviously "a bunch" of iron (an element known by the chemical symbol Fe) weighs more than "a bunch" of oxygen, but what exactly is "a bunch"? Italian physicist Amedeo Avogadro (1776-1856), the first scientist to clarify the distinction between atoms and molecules, created a unit that made it possible to compare the masses of various molecules. This is the mole, also known as "Avogadro's number," a unit equal to 6.022137 × 10 23 (more than 600 billion trillion) molecules.
The term "mole" can be used in the same way that the word "dozen" is used. Just as "a dozen" can refer to twelve cakes or twelve chickens, so "mole" always describes the same number of molecules. A mole of any given substance has its own particular mass, expressed in grams. The mass of one mole of iron, for instance, will always be greater than that of one mole of oxygen. The ratio between them is exactly the same as the ratio of the mass of one iron atom to one oxygen atom. Thus, the mole makes it possible to compare the mass of one element or compound to that of another.
M OLECULAR A TTRACTION AND M OTION
Molecular dynamics can be understood primarily in terms of the principles of motion, identified by Sir Isaac Newton (1642-1727), principles that receive detailed discussion at several places in this volume. However, the attraction between particles at the atomic and molecular level cannot be explained by reference to gravitational force, also identified by Newton. For more than a century, gravity was the only type of force known to physicists, yet the pull of gravitation alone was too weak to account for the strong pull between atoms and molecules.
During the eighteenth century and early nineteenth centuries, however, physicists and other scientists became increasingly aware of another form of interaction at work in the world—one that could not be explained in gravitational terms. This was the force of electricity and magnetism, which Scottish physicist James Clerk Maxwell (1831-1879) suggested were different manifestations of a "new" kind of force, electromagnetism. All subatomic particles possess either a positive, negative, or neutral electrical charge. An atom usually has a neutral charge, meaning that it is composed of an equal number of protons (positive) and electrons (negative). In certain situations, however, it may lose one or more electrons and, thus, acquire a net charge, making it an ion.
Positive and negative charges attract one another, much as the north and south poles of two different magnets attract. (In fact, magnetism is simply an aspect of electromagnetic force.) Not only do the positive and negative elements of an atom attract one another, but positive elements in atoms attract negative elements in other atoms, and vice versa. These interactions are much more complex than the preceding discussion suggests, of course; the important point is that a force other than gravitation draws matter together at the atomic and molecular levels. On the other hand, the interactions that are critical to the study of molecular dynamics are primarily mechanical, comprehensible from the standpoint of Newtonian dynamics.
MOLECULAR BEHAVIOR AND PHASES OF MATTER.
All molecules are in motion, and the rate of that motion is affected by the attraction between them. This attraction or repulsion can be though of like a spring connecting two molecules, an analogy that works best for solids, but in a limited way for liquids. Most molecular motion in liquids and gases is caused by collisions with other molecules; even in solids, momentum is transferred from one molecule to the next along the "springs," but ultimately the motion is caused by collisions. Hence molecular collisions provide the mechanism by which heat is transferred between two bodies in contact.
The rate at which molecules move in relation to one another determines phase of matter—that is, whether a particular item can be described as solid, liquid, or gas. The movement of molecules means that they possess kinetic energy, or the energy of movement, which is manifested as thermal energy and measured by temperature. Temperature is really nothing more than molecules in motion, relative to one another: the faster they move, the greater the kinetic energy, and the greater the temperature.
When the molecules in a material move slowly in relation to one another, they tend to be close in proximity, and hence the force of attraction between them is strong. Such a material is called a solid. In molecules of liquid, by contrast, the rate of relative motion is higher, so the molecules tend to be a little more spread out, and therefore the force between them is weaker. A material substance whose molecules move at high speeds, and therefore exert little attraction toward one another, is known as a gas. All forms of matter possess a certain (very large) amount of energy due to their mass; thermal energy, however, is—like phase of matter—a function of the attractions between particles. Hence, solids generally have less energy than liquids, and liquids less energy than gases.