Chemistry
Structure of Organic Molecules
The structure of organic molecules refers to the arrangement of atoms within a molecule. Organic molecules are composed of carbon atoms bonded to other atoms such as hydrogen, oxygen, nitrogen, and sulfur. The arrangement of these atoms and the types of bonds between them determine the physical and chemical properties of the molecule.
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9 Key excerpts on "Structure of Organic Molecules"
eBook - PDF- T. W. Graham Solomons, Craig B. Fryhle, Scott A. Snyder(Authors)
- 2017(Publication Date)
- Wiley(Publisher)
The Basics BONDING AND MOLECULAR STRUCTURE C H A P T E R 1 Organic chemistry plays a role in all aspects of our lives, from the clothing we wear, to the pixels of our television and computer screens, to preservatives in food, to the inks that color the pages of this book. If you take the time to under- stand organic chemistry, to learn its overall logic, then you will truly have the power to change society. Indeed, organic chemistry provides the power to synthesize new drugs, to engineer molecules that can make computer processors run more quickly, to understand why grilled meat can cause cancer and how its effects can be combated, and to design ways to knock the calories out of sugar while still making food taste deliciously sweet. It can explain biochemical processes like aging, neural functioning, and cardiac arrest, and show how we can prolong and improve life. It can do almost anything. IN THIS CHAPTER WE WILL CONSIDER: • what kinds of atoms make up organic molecules • the principles that determine how the atoms in organic molecules are bound together • how best to depict organic molecules ▸ WHY DO THESE TOPICS MATTER? At the end of the chapter, we will see how some of the unique organic structures that nature has woven together possess amazing properties that we can harness to aid human health. 1 photo credits: computer screen: Be Good/Shutterstock; capsules: Ajt/Shutterstock 2 CHAPTER 1 THE BASICS: Bonding and Molecular Structure Organic chemistry is the chemistry of compounds that contain the element carbon. If a compound does not contain the element carbon, it is said to be inorganic. Look for a moment at the periodic table inside the front cover of this book.
eBook - PDF- T. W. Graham Solomons, Craig B. Fryhle, Scott A. Snyder(Authors)
- 2022(Publication Date)
- Wiley(Publisher)
1 CHAPTER 1 Chakrapong Worathat/123RF studiovin/Shutterstock The Basics Bonding and Molecular Structure Organic chemistry plays a role in all aspects of our lives, from the reactions that keep us alive, to medicines that fight disease, to materials for new technologies such as high definition tele- visions. If you take the time to understand organic chemistry, you will truly have the power to change society. Indeed, organic chemistry, provides the power to synthesize new drugs, to engineer molecules that can make computer processors run more quickly, to understand why grilled meat can cause cancer and how its effects can be combated, and to design ways to knock the calories out of sugar while still making food taste deliciously sweet. It can explain biochemical processes like aging, neural functioning, and cardiac arrest and show how we can prolong and improve life. It can do almost anything. IN THIS CHAPTER WE WILL CONSIDER: • what kinds of atoms make up organic molecules • the principles that determine how the atoms in organic molecules are bound together • how best to depict organic molecules WHY DO THESE TOPICS MATTER? At the end of the chapter, we will see how some of the unique organic structures that nature has woven together possess amazing properties that we can harness to aid human health. See the online course materials in for additional examples, videos, and practice. 2 CHAPTER 1 The Basics Organic chemistry is the chemistry of compounds that contain the element carbon. If a compound does not contain the element carbon, it is said to be inorganic. Look for a moment at the periodic table. More than a hundred elements are listed there.
eBook - PDF- T. W. Graham Solomons, Craig B. Fryhle, Scott A. Snyder(Authors)
- 2016(Publication Date)
- Wiley(Publisher)
BONDING AND MOLECULAR STRUCTURE The Basics C H A P T E R 1 Organic chemistry plays a role in all aspects of our lives, from the clothing we wear, to the pixels of our television and computer screens, to preservatives in food, to the inks that color the pages of this book. If you take the time to under- stand organic chemistry, to learn its overall logic, then you will truly have the power to change society. Indeed, organic chemistry provides the power to synthesize new drugs, to engineer molecules that can make computer processors run more quickly, to understand why grilled meat can cause cancer and how its effects can be combated, and to design ways to knock the calories out of sugar while still making food taste deliciously sweet. It can explain biochemical processes like aging, neural functioning, and cardiac arrest, and show how we can prolong and improve life. It can do almost anything. IN THIS CHAPTER WE WILL CONSIDER: • what kinds of atoms make up organic molecules • the principles that determine how the atoms in organic molecules are bound together • how best to depict organic molecules [ WHY DO THESE TOPICS MATTER? ] At the end of the chapter, we will see how some of the unique organic structures that nature has woven together possess amazing properties that we can harness to aid human health. See for additional examples, videos, and practice. 1 photo credits: computer screen: Be Good/Shutterstock; capsules: Ajt/Shutterstock 2 CHAPTER 1 THE BASICS: Bonding and Molecular Structure Organic chemistry is the chemistry of compounds that contain the element carbon. If a compound does not contain the element carbon, it is said to be inorganic. Look for a moment at the periodic table inside the front cover of this book.
eBook - PDF- Arne Engström, J. B. Finean(Authors)
- 2013(Publication Date)
- Academic Press(Publisher)
C H A P T E R Iii The Principles of Molecular Structure The foundations of molecular structure were laid by chemists using es-sentially chemical methods to study the composition of chemical compounds and their reactions. Long before anything was known of the structure of the atom, chemists had begun to summarize the chemical data in terms of a structural formula which showed the relative proportions in which the ele-ments combined. Each element was represented by a letter, and the constit-uent atoms were linked by a line which symbolized a definite chemical union. The development of stereochemistry indicated that these links be-tween atoms had definite orientations in space, and it was soon clear that each atom had a specific number of valencies directed at specific angles with respect to each other. Thus developed the field of study of structural chemistry in which the aim was to describe individual structures in terms of the precise relationships between its constituent atoms. This study involves both the spatial or geometrical relationships among the constituent atoms and the forces holding them in these fixed relative positions. The field of biological ultrastructure is formally concerned with the spatial relation-ships, but as these are a direct result of the forces acting between the sim-pler constituents, a preliminary appreciation of these forces is essential to the understanding of structural data. The modern concept of these forces is summarized in the electronic theory of valency, which is treated in detail in textbooks on structural chemistry, but here will be abbreviated to a de-scription of the aspects important for general structural considerations.
eBook - PDFChemistry
The Molecular Nature of Matter
- Neil D. Jespersen, Alison Hyslop(Authors)
- 2014(Publication Date)
- Wiley(Publisher)
At the molecular level of life, nature uses compounds of carbon. The amazing variety of living systems, down to the uniqueness of each individual, is possible largely because of the prop- erties of this element. In this chapter we will introduce you to organic chemistry. LEARNING OBJECTIVES After reading this chapter, you should be able to: • write structural formulas for organic compounds, highlighting their functional groups • describe the nomenclature rules and major reactions of alkanes, alkenes, alkynes, and aromatic hydrocarbons • describe the names and typical reactions of common alcohols, ethers, aldehydes, ketones, carboxylic acids, and esters • describe the names and typical reactions of amines and amides • explain the structures, synthesis, and properties of polymers • name common carbohydrates, lipids, and proteins and describe their properties • explain how the structures of DNA and RNA enable the transmission of genetic information and the synthesis of proteins 22.1 | Organic Structures and Functional Groups Organic chemistry is the study of the preparation, properties, and reactions of those compounds of carbon not classified as inorganic. The latter include the oxides of carbon, the bicarbonates and carbonates of metal ions, the metal cyanides, and a handful of other compounds. There are tens of millions of known carbon compounds, and all but a very few are classified as organic. Uniqueness of the Element Carbon What makes the existence of so many organic compounds possible is the ability of carbon atoms to form strong covalent bonds to each other while at the same time bonding strongly to atoms of other nonmetals. For example, molecules in the plastic polyvinylchloride, which is used to make the polymer beads in the chapter-opening photograph, have carbon chains that are thousands of carbon atoms long, with hydrogen and chlorine atoms attached to the carbon atoms. polyvinylchloride (small segment of one molecule) C C C H H etc.
eBook - PDFGeneral, Organic, and Biological Chemistry
An Integrated Approach
- Kenneth W. Raymond(Author)
- 2012(Publication Date)
- Wiley(Publisher)
After completing this chapter, you should be able to: A n Introduction to Organic Compounds CHAPTER 4 OBJECTIVES ABOUT THIS CHAPTER 4 118 CHAPTER 4 An Introduction to Organic Compounds 4.1 S T R U C T U R A L F O R M U L A S Before we can consider organic molecules, we must expand on the discussion of covalent bonds and molecules that was initiated in Chapter 3. Section 3.5 introduced molecules, the uncharged groups of nonmetal atoms that are connected to one another by covalent bonds, and showed that the structure of a given molecule can be represented by an elec- tron dot structure (all valence electrons are shown using dots) or a Lewis structure (each pair of shared bonding electrons is represented by a line). In the structures of isopropyl alcohol (rubbing alcohol) shown below, the carbon atoms and oxygen atom have formed the number of covalent bonds required to reach an octet—four bonds for carbon atoms and two bonds for oxygen atoms. Electron dot structure Lewis structure H¬ H ƒ C ƒ H ¬ H ƒ C ƒ O ƒ H ¬ H ƒ C ƒ H ¬H H H C H H C O H H C H H Isopropyl alcohol Either of these structural formulas provides more information about isopropyl alco- hol than does the molecular formula (C 3 H 8 O), because molecular formulas tell nothing about how atoms are attached to one another. Suppose, for example, that a toxicologist is reporting on the health problems associated with exposure to high levels of the compound C 3 H 8 O. Because this molecular formula does not tell us how the molecule is put together, it is not clear whether she is talking about isopropyl alcohol or one of the other two mol- ecules that have the same molecular formula. Representing the molecule using a structural formula (Figure 4.1) clarifies the matter. Given a molecular formula, how do we go about drawing a structural formula? For small molecules, knowing the number of covalent bonds that an atom is expected to form can be a good place to start.
eBook - PDF- Douglas Henderson(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
The 1 2 S. H. Bauer current trend is to characterize intramolecular motions in detail by means of specific distribution and correlation functions. Also, there is ample recognition by chemists that while for each combination of atoms there is a three-dimensional arrangement of nuclei for which the total energy is a minimum, there often exist closely similar arrangements at adjacent energy minima which are separated by relatively low barriers. Prior to considering the variety of physical techniques now in use by chemists for molecular-structure investigations it will prove instructive to note their interrelationship and to indicate which questions are answered by each method. For purposes of identification of any molecular species it is necessary to specify which atom in the molecule is bonded by valence forces'' to what other atoms. This was the major problem of Kekulé, Couper, Butlerov, and their contemporaries (see Kazansky and Bykov (1961)). The answers are of a topological nature. For compounds which consist primarily of hydrogen and carbon, with occasional N, O, S, and Ρ atoms, organic chemists have developed ingenious techniques for the determi-nation of connectivity. One of the fundamental points was the early recognition of the existence of isomers for all but the simplest molecular species. * A prerequisite of this approach is the acceptance of rules of valence and the principle of minimum structural and configurational change induced by carefully selected structure-probing reactions. The method of classical structure analysis may be applied with reliability to organic compounds because of the covalent nature of their bonding; its extension to compounds which include the elements in the upper right-hand corner of the periodic table and to the metalloorganics proved quite successful.
eBook - PDFMolecular Design
Chemical Structure Generation from the Properties of Pure Organic Compounds
- A.L. Horvath(Author)
- 2012(Publication Date)
- Elsevier Science(Publisher)
(Motoc, 1983). When two or several atoms interact and bond to each other on a stable arrangement, they form definite groups of atoms or molecules. The size of the molecules are usually given as longest 106 dimensions, see Fig. 1.6.1. The crystal ionic radii may be expressed in nm (nonameter, 10 9 m; 1 A = 10 10 m) units, see Table 1.6.1. Large numbers of natural and synthetic substances are composed of a great number of atoms which are made up of very large often called macromolecules or high polymers. The organic compounds are formed on the ability of the carbon atoms to build chains and rings in which various numbers of carbon atoms are linked together. In different organic molecules the chains and rings may have side-chains in various positions creating large numbers of isomeric compounds, that is, the same number of carbon, hydrogen, etc. atoms in the molecule but with different geometrical arrangements. The isomerizms are already discussed in chapter 1.4. As described in chapter 1.1, the methane molecule is composed of one carbon atom which is connected by four valency bonds to four hydrogen atoms. These valency bonds form an angle of approximately 109° to each other in a three dimensional arrangement. The hydrogen atoms are not linked to each other chemically, therefore they tend to repel each other. The repulsion increases as the atoms are closer to one other. Consequently, the three dimensional structure of methane is represented by the maximum distance between the hydrogen atoms, bearing in mind that the C-H bonds are of the same lengths. In ethane molecule (CH 3 -CH 3 ) the valency bonds have the same angles as in methane. However, the molecule can rotate about the single bond which joins the two carbon atoms. The two conformations of the molecular structure are called eclipsed and staggered conformations. In the first conformation the C-H bonds of the two carbon atoms are in line with one other.
eBook - PDF- Brian W. Pfennig(Author)
- 2021(Publication Date)
- Wiley(Publisher)
H 1s H 1s H 1s H 1s sp 3 sp 3 sp 3 sp 3 C 7 Structure and Bonding in Molecules “Attempts to regard a molecule as consisting of specific atoms or ionic units held together by discrete numbers of bonding electrons or electron pairs are considered as more or less meaningless.” —Robert Mulliken 7.1 MOLECULES AS UNIQUE ENTITIES Previously, we defined a chemical bond as the way in which the electron density is distributed between one or more atoms to form a molecule. Suppose that I were to ask one of my students to sketch a molecule. Most likely, they would invoke a ball and spoke model where the atoms are represented by spheres of an appro- priate size and the bonds are represented as spokes (or lines) connecting these atoms together. This is the way that our minds have been programmed over the years to visualize molecules. However, we have already shown examples of molecules where the electrons are not, in fact, localized between two and only two atoms; for example, the (3c–2e) bonding in diborane. It is indeed unfortunate that the simplicity of Lewis structures hampers our ability to grasp the richness and complexity of atomic interactions in molecules already set forth in the quan- tum theory of atoms in molecules. The QTAIM model takes a holistic approach where the topology of the molecule can be used to apportion the overall electron density between the nuclei. The zero-flux gradient paths can be used to separate the electron density into atomic basins representing the more realistic (and non- spherical) shapes of atoms in molecules. After a certain point, however, the atoms essentially lose their individualistic properties and the focus shifts to the structure and properties of the molecule as a whole. In fact, it would greatly benefit the reader of this textbook to come to the realization that a molecule is indeed a separate entity from the individual atoms that comprise it.
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