The Molecular Structure of Matter

Matt Strassler [May 28, 2012]

In any of the world’s great libraries, the rooms and shelves of books stretch on seemingly without end. The tomes in the United States’ Library of Congress number in the tens of millions. Each of them presents a distinct story, or a detailed analysis, or a historical document, with its own individual meaning. Yet these millions of books written in the English language are constructed from a mere few tens of thousands of words, and each of these words is written using a combination of just 26 letters — the letters A through Z.

Meanwhile, we live surrounded by a vast and astonishing diversity of materials — not the least fantastic of which are the many types of biological structures that make up our own bodies and those of all other animals, plants, and other living creatures. The planet on which we live is made from all sorts of rocks, some hard and brittle, some malleable, of many colors and textures. In addition to water we encounter alcohols, acids, sugars and oils of various forms. The food cooking on our stoves produces all sorts of aromas for us to inhale, floating amid the air we breathe.  To salts and chalks and alloys, we must add new, synthetic materials, such as the many types of plastics.  But it is important to remember that the vast contents of this Library of Materials are all constructed from a smaller (though still very large) assortment of molecules, themselves formed from a mere 100 or so atoms — the elements H through U (hydrogen through uranium, and beyond).

The complexity of a written language like English rests on words, and the complexity of materials begins with molecules. (Similarly, the instructions for building a vast array of biological forms can be encoded on DNA — dioxyribonucleic acid — specifically, in its strings of three-molecule syllables constructed from four basic molecules, called “nucleobases”.) The source of this complexity rests on the simple mathematical fact that a huge number of possible combinations can arise even a small number of ingredients. A single ingredient is not enough. From the letter “a” alone, only ten potential words can be constructed with ten letters or less: “a”, “aa”, “aaa”’, and so forth. But with 26 letters, the number of potential two-letter words is already 26 squared, or 676, and the number of potential ten-letter words is 141,167,095,653,376, immensely more than needed for language. Similarly, just a few tens of thousands of words, chosen from within these many millions of billions of potential words, are more than enough to create all of English literature. The same principles of exponential growth in the numbers of combinations allow all of our earthly surroundings to be formed out of a hundred types of atoms, which can be combined in an unlimited array of molecules ranging in size from just a few atoms to many hundreds or even thousands.

Starting from words, or molecules, we may seek insights by working in one of two directions.  We may try to comprehend how it is that complex objects are assembled from these ingredients: what lies behind the existence of an individual book, or a set of books? what is the origin of a given material or class of materials? Or we may instead try to work the other direction, and establish the origin of the letters and atoms that are the essential building blocks.

The purpose of this webpage and the pages below it is to address the second question, from molecules down to their origins. Fascinating as it is to study the enormous range of materials found in nature, it is as vast a subject as the Library of Congress itself. The origin of molecules and atoms, on the other hand, turns out to be a smaller and more manageable topic. This is not to say that the answer is straightforward or simple! Instead, it brings us into the many surprising and fascinating details of atomic, nuclear, and “particle” (or “high-energy”) physics. And as is the case for the origin of the letters of the alphabet, the answer turns out to have much larger and more interesting implications than one might immediately have guessed. For it leads us to profound insights into far more than ordinary materials… guiding physicists to an understanding of light, of the sun and the other stars, of the earth’s history, of space and time, and of the wider universe through which the earth and sun are traveling.

Before we move on, there are a couple of questions that ought to be addressed. How do we know that all materials are made from molecules? Historically, the answer was obtained through sophisticated chains of logic and a huge variety of scientific tests. Until very recently, the existence of molecules was something that could only be inferred, indirectly but convincingly, from clever scientific analysis of vast numbers of chemistry experiments. But a more straightforward answer can be given today, for it is becoming possible today to “see” the molecules. We see them with microscopes, though not the classic sort you put on a laboratory table and peer into with your eyes. These types of microscopes are called atomic force microscopes, and their way of seeing is more like reading braille; but they do the job.  They allow scientists to make pictures of materials, and see their structure in detail, confirming prior predictions for that structure.  They have even permitted confusions about particular molecules to be resolved.  These new methods allow a very direct check of all the indirect arguments.  Not that those arguments were ever in doubt, since they were so often applied successfully in the prediction of chemical reactions and in the design and construction of new materials! But still, it’s good to know that this discussion is not an abstract one: molecules really exist, and we can detect them directly with modern technology.

Now let’s move on to atoms: what are they made of, and how do they form molecules?

14 responses to “The Molecular Structure of Matter

  1. Dear Professor,

    Thank you for the alphabet and library analogy, it does convey an explosion of scale vividly, as well as an explosion of diversity.

    Every analogy invites my imagination to probe its limits. (I think all analogies have limits; it’s usually best not to be distracted by them.) I recall, though, some of the missing energy analogies we’ve discussed in the past, where an observer of one dimension deduces an unobserved dimension by measuring energy. So I wonder, if we have an analogous Library of Congress, and we start to understand English, we’ll also understand what is not English. When we learn to recognize English pretty well, we can subtract it out and discover other languages that are hidden in the larger signal.

    Perhaps the LHC trigger is analogous to an English detector? And the Library of Congress is an inverse Barn? (Perhaps I’ve gone too far.)

  2. Very interesting and enjoyable post. Thanks for sharing.

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  6. Professor, your link at the bottom of your posting leads to an oops page.

  7. I’d add to this or the next article another question: “Why do molecules stick together to make matter?”

  8. Excellent introductory text. You may want to fix the following sentence, “The source of this complexity rests on the simple mathematical fact that a huge number of possible combinations can arise [from] even a small number of ingredients.” Please delete this comment.

  9. Wolfgang Vogelbein

    Dear Professor, please correct a spelling error “…can be encoded on DNA — dioxyribonucleic acid —”. The correct spelling is DE(S)oxyribonucleic acid, meaning that an atom of oxygen has been removed from ribose (a sugar, and one of the components of DNA). Your spelling implies that two atoms of oxygen have been added – a big difference.

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  13. Fascinating. As Mr Spock might say

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