What Do Molecules Look Like

Molecules are far too small for us to observe them directly. An effective means of visualizing them is by the use of molecular models. Throughout this book, we will represent matter at the molecular level using molecular art, the two-dimensional equivalent of molecular models. In these pictures, atoms are represented as spheres and atoms of particular elements are represented using specific colors. Table 1.1 lists some of the elements that you will encounter most often and the colors used to represent them in this book. 

TABLE 1.1 Colors of Elements Commonly Used m Molecular Ait 

Although it can take many different forms, all matter consists of various combinations of atoms of only a relatively small number of simple substances called elements. The properties of matter depend on which of these elements it contains and on how the atoms of those elements are arranged. 

Natural phenomena and measured events if universally consistent, can be stated as a. law 

Having contracted cowpox, milkmaids have a natural immunity to smallpox. 

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What Do Molecules Look Like 5 How Important Are Units 14... 

I hope Fve been able to give you an idea of the grand challenges and grand excitement that is chemistry these days. It s a way of thinking about the world, right down to the level of molecules. I always tell my students I want them to think like molecules —what do molecules look like, what do they want to do, and why do they want to do that If you can think like a molecule, then you might be able to convince molecules to do what you want them to do. Then you re a chemist. 

Porphyrins are purple and they are pigments. Such characteristics, however, apply to several dye molecules. What is it that makes porphyrins special Through heme, an iron porphyrin, they are intimately associated with blood, and many of the redox enzymes involved in metabolic processes. Through chlorophyll, a reduced magnesium porphyrin, they orchestrate photosynthesis, without which life as we know it would be impossible. So what do porphyrins look like ... 

Among the 16 million that have been made, there are all kinds of molecules with amazingly varied properties. What do they look like They may be crystalline solids, oils, waxes, plastics, elastics, mobile or volatile liquids, or gases. Familiar ones include sugar, a cheap natural compound isolated from plants as hard white crystals when pure, and petrol, a mixture of colourless, volatile, flammable hydrocarbons. Isooctane is a typical example and gives its name to the octane rating of petrol. 

The first several chapters of any organic chemistry textbook focus on the structure of molecules how atoms connect to form bonds, how we draw those connections, the problems with our drawing methods, how we name molecules, what molecules look like in 3D, how molecules twist and bend in space, and so on. Only after gaining a clear understanding of stracture do we move on to reactions. But there seems to be one exception acid-base chemistry. 

Experiments cannot tell us what transition states look like. The fact is that transition states cannot even be detected experimentally let alone characterized, at least not directly. While measured activation energies relate to the energies of transition states above reactants, and while activation entropies and activation volumes, as well as kinetic isotope effects, may be invoked to imply some aspects of transition-state structure, no experiment can actually provide direct information about the detailed geometries and/or other physical properties of transition states. Quite simply, transition states do not exist in terms of a stable population of molecules on which experimental measurements may be made. Experimental activation parameters provide some guide, but tell us little detail about what actually transpires in going from reactants to products. 

As we have seen, the number of possible organic compounds is virtually limitless. How can anyone learn the chemistry of all of them Fortunately, we do not need to learn an entire new set of chemical reactions for each new compound encountered. A particular arrangement or group of atoms has very similar chemistry no matter what the remainder of the molecule looks like. 

Real-World Question What do sugar molecules look like ... 

What does a water molecule look like It isn t possible to see a single molecule, but in Chapter 4, you used a covalent bonding model to explain how two hydrogen atoms and one oxygen atom bond together to form the water molecule. Does this model teU anything about the shape of the molecule It s important to find out because the bonding patterns and the shapes of all molecules have a lot to do with their properties. 

Note that resonance structures do not exist as independent molecules they only serve to approximate what the real molecule looks like. That is, the molecule is actually a hybrid of its resonance structures. 

The molecule vibrates back and forth across that equilibrium geometry, and our next task is to describe what those motions look like. Which atoms are moving, and in what directions And how many different kinds of motion do we need to consider ... 

Compare the Lewis diagrams with the three-dimensional representations of the molecules. Notice that the molecules are three-dimensional—they do not look like their two-dimensional Lewis diagrams. All bond angles are tetrahedral. Thus what appears to be a nice straight line of carbon atoms in a Lewis diagram is actually a zigzag chain of carbon atoms. 

We do see water an aggregate of tiny water molecules. We are able to see the molecules, all right, but not an individual molecule. It is too minute to see with our naked eyes. So, are the atoms and the molecules for real Chemists assume and also believe that they are. What do atoms or molecules look like Chemists picture them based on the atoms and their combination, as we did in the last two chapters and do throughout this book. Can we see them Seeing is believing, isn t it But the atoms and molecules are too small to be seen with our naked eyes. So what should we do Magnify them ... 

How do chemists know what molecules look like if they are too small to see with even the most advanced microscope The answer is spectroscopy. Basically, we shine light of various frequencies on a pure sample of a molecule, and based on what happens to that light we can make various inferences about the structure of the molecule. IR spectroscopy is the first of several spectroscopic methods we will study in this course. The next one, called NMR, is much more powerful and will (unlike IR) allow us to elucidate the entire structure of some simple molecules. 

For molecules similar to safrole or allylbenzene we take the work done on any terminal alkene such as 1-heptene, 1 octene. Another term to look for is olefin which is a term for a doublebond containing species. What we then look for are articles about these olefins where the functional groups we are looking for are formed. Articles with terminology like methyl ketones from (P2P), ketones from , amines from etc. Or when we want to see about new ways to aminate a ketone (make final product from P2P) we look for any article about ketones where amines are formed. Sound like science fiction to you Well, how do you think we came up with half the recipes in this book It works ... 

Now, for simple molecules like propane, this is not much of an improvement. It is easier to draw, but the reader has to do some thinking to figure out what the molecule is. However, with larger molecules, the simplification really helps to keep the picture uncluttered. Consider the molecule for aspartame, which would look like this ... 

The data collected are subjected to Fourier transformation yielding a peak at the frequency of each sine wave component in the EXAFS. The sine wave frequencies are proportional to the absorber-scatterer (a-s) distance /7IS. Each peak in the display represents a particular shell of atoms. To answer the question of how many of what kind of atom, one must do curve fitting. This requires a reliance on chemical intuition, experience, and adherence to reasonable chemical bond distances expected for the molecule under study. In practice, two methods are used to determine what the back-scattered EXAFS data for a given system should look like. The first, an empirical method, compares the unknown system to known models the second, a theoretical method, calculates the expected behavior of the a-s pair. The empirical method depends on having information on a suitable model, whereas the theoretical method is dependent on having good wave function descriptions of both absorber and scatterer. 

What do the molecules of a solid surface look like, and how are the characteristics of these different from the bulk molecules In the case of crystals, one asks about the kinks and dislocations. 

In contrast, in most heterogeneous reactions, we really do not even understand what one of the reactants, the surface, looks like on a molecular level i.e., the condensed-phase molecule and its environment that the incoming gaseous reactant encounters is not well characterized. An example of our incomplete understanding of the nature of surfaces is controversy about effective surface areas for ice and whether ice surfaces prepared in the laboratory for example, are porous or not (e.g., see Keyser et al., 1993 and Hanson and Ravishankara, 1993a). 

The Fourier series that the crystallographer seeks is p(x,y,z), the three-dimensional electron density of the molecules under study. This function is a wave equation or periodic function because it repeats itself in every unit cell. The waves described in the preceeding equations are one-dimensional they represent a numerical value/(x) that varies in one direction, along the x-axis. How do we write the equations of two-dimensional and three-dimensional waves First, what do the graphs of such waves look like ... 

Quantum mechanics calculations are more expensive to carry out because they require considerable more computing power and time than molecular mechanics calculations. Consequently, molecular mechanics is the more useful source of the large structures of interest to the medicinal chemist and so this chapter will concentrate on this method. To save time and expense, structures are often built up using information obtained from databases, such as the Cambridge and Brookhaven databases. Information from databases may also be used to check the accuracy of the modelling technique. However, in all cases, the accuracy of the structures obtained will depend on the accuracy of the data used in their determination. Furthermore, it must be appreciated that the molecular models produced by computers are a caricature of reality that simply provide us with a useful picture for design and communication purposes. It is important to realize that we still do not know what molecules actually look like ... 

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