《有机化学》课程教学资源（参考书籍）Organic chemistry with biological applications, 3ed-Gengage Learning, John E. McMurry, Brooks Cole（2015）.pdf_P26-P30

lowering our cholesterol level means limiting the amount that our bodies biosynthesize, which in turn means understanding and controlling the chemical reactions that make up the metabolic pathway for cholesterol biosynthesis. Now look at FigUre 1.1. Although the figure probably looks unintelligible at this point, don’t worry; before long it will make perfectly good sense. What’s shown in Figure 1.1 is the biological conversion of a compound called 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) to mevalonate, a crucial step in the pathway by which our bodies synthesize cholesterol. Also shown in the figure is an X-ray crystal structure of the active site in the HMG-CoA reductase enzyme that catalyzes the reaction, along with a molecule of the drug atorvastatin (sold under the trade name Lipitor), which binds to the enzyme and stops it from functioning. With the enzyme thus inactivated, cholesterol biosynthesis is prevented. HO H H CH3 CH3 CO2 – H H Cholesterol Atorvastatin (Lipitor) 3-Hydroxy-3-methyl- Mevalonate glutaryl coenzyme A (HMG-CoA) H H3C OH OH –O2C H3C OH O SCoA C CH3 CH3 O F 3.0 3.2 3.0 2.7 2.7 Lα4 Sβ4 K735 L967 L853 V683 S684 R590 D690 K691 K692 A850 R508 D586 L562 R556 H752 Lα1 Lα6 Lα10 2.5 2.9 2.8 2.8 2.9 N N H CO2 – OH HO H H Atorvastatin is one of a widely prescribed class of drugs called statins, which reduce a person’s risk of coronary heart disease by lowering the level of cholesterol in his or her blood. Taken together, the statins—atorvastatin (Lipitor), simvastatin (Zocor), rosuvastatin (Crestor), pravastatin (Pravachol), lovastatin (Mevacor), and several others—are the most widely prescribed drugs in the world, with global sales of $29 billion annually. The statins function by blocking the HMG-CoA reductase enzyme and preventing it from converting HMG-CoA to mevalonate, thereby limiting the body’s biosynthesis of cholesterol. As a result, blood cholesterol levels drop and coronary heart disease becomes less likely. It sounds simple, but it would FigUre 1.1 how does atorvastatin control cholesterol biosynthesis? The metabolic conversion of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) to mevalonate is a crucial step in the body’s pathway for biosynthesizing cholesterol. An X-ray crystal structure of the active site in the HMGCoA reductase enzyme that catalyzes the reaction is shown, along with a molecule of atorvastatin (Lipitor) that is bound in the active site and stops the enzyme from functioning. With the enzyme thus inactivated, cholesterol biosynthesis is prevented. Unless otherwise noted, all content on this page is © Cengage Learning. 2 chapter 1 Structure and Bonding 42912_01_Ch01_0001-0027h.indd 2 1/10/14 11:40 AM Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

1-1 ATOMIC STRUCTURE:THE NUCLEUS nway fo without doailed knowledge of the steps in the pa ely shar an be w pre c is wha ally.th es it all ha h。 ch organi nistry dates to the late 1700 when at that tir nd the gaof th lants and ani als so ned diff ent fr hat of the sinor es found in min were generally lov .melting solids an sually more urify and work with than in nic co inds.By the mid 1800s however it was clear that there was no fundamental difference betweer organic and inorganic compounds:the same principles explain the behaviors of all substances,regardless of origin or complexity.The only distinguishing characteristic of organic chemicals is that all contain the element carbon But why is carbon special?Why,of the more than 70 million presently known chemical compounds,do more than 99%of them contain carbon?The answers to these questions come from carbon's electronic structure and its con. sequent position in the periodic table(FIGURE 1.2).As a group 4A element. carbon can share four valence electrons and form four strong covalent bonds Furthermore,carbon atoms can bond to one another,forming long chains and rings.Carbon,alon e of all elements,is able to form an immense diversity o compounds,from the simple to the staggeringly comple om met ane,with one carbon atom,to DNA,which can have more than 100 million carbons FIGURE1.2 Elements comm nds.C d in organic 3A 4A 5A 6A 7A and other elements Li Be e commonly found in organic ompounds are shown i Na Mg Si s c the col typically used to K ca Sc Ti V Cr Mn Fe Co Ni cu Zn Ga Ge As se Br Rb Sr Zr Nb Mo Tc Ru Rh Pd Ag cd In Sn Te + Cs Ba La Hf Ta w Re Os Ir Pt Au Hg TI Pb Bi Po At Rn Fr Ra Ac Not all carbon compounds are derived from living organisms of course Modern chemists have develoned a remarkably s ophisticated ability to design and synthesize new organic compounds in the laboratory-medicines,dyes RamnayaatcamiegOahesryoaehshoa 11 Atomic Structure:The Nucleus (FICURE 13) Unless content on this page isCenoage Leaming

be impossible without detailed knowledge of the steps in the pathway for cholesterol biosynthesis, the enzymes that catalyze those steps, and how precisely shaped organic molecules can be designed to block those steps. Organic chemistry is what makes it all happen. Historically, the term organic chemistry dates to the late 1700s, when it was used to mean the chemistry of compounds found in living organisms. Little was known about chemistry at that time, and the behavior of the “organic” substances isolated from plants and animals seemed different from that of the “inorganic” substances found in minerals. Organic compounds were generally low-melting solids and were usually more difficult to isolate, purify, and work with than high-melting inorganic compounds. By the mid- 1800s, however, it was clear that there was no fundamental difference between organic and inorganic compounds: the same principles explain the behaviors of all substances, regardless of origin or complexity. The only distinguishing characteristic of organic chemicals is that all contain the element carbon. But why is carbon special? Why, of the more than 70 million presently known chemical compounds, do more than 99% of them contain carbon? The answers to these questions come from carbon’s electronic structure and its consequent position in the periodic table (FigUre 1.2). As a group 4A element, carbon can share four valence electrons and form four strong covalent bonds. Furthermore, carbon atoms can bond to one another, forming long chains and rings. Carbon, alone of all elements, is able to form an immense diversity of compounds, from the simple to the staggeringly complex—from methane, with one carbon atom, to DNA, which can have more than 100 million carbons. Li O Group 1A H Na K Rb Cs Fr Be 2A Mg Ca Sr Ba Ra B Al Ga In Tl Si P C N Ge Sn Pb As Sb Bi S Se Te Po F Cl Br I At Ne Ar He 3A 4A 5A 7A 6A 8A Kr Xe Rn Sc Y La Ti Zr Hf V Nb Ta Cr Mo W Mn Tc Re Fe Ru Os Co Rh Ir Ni Pd Pt Cu Ag Au Zn Cd Hg Ac Not all carbon compounds are derived from living organisms of course. Modern chemists have developed a remarkably sophisticated ability to design and synthesize new organic compounds in the laboratory—medicines, dyes, polymers, and a host of other substances. Organic chemistry touches the lives of everyone; its study can be a fascinating undertaking. 1-1 atomic Structure: the nucleus As you might remember from your general chemistry course, an atom consists of a dense, positively charged nucleus surrounded at a relatively large distance by negatively charged electrons (FigUre 1.3). The nucleus consists FigUre 1.2 elements commonly found in organic compounds. Carbon, hydrogen, and other elements commonly found in organic compounds are shown in the colors typically used to represent them. Unless otherwise noted, all content on this page is © Cengage Learning. 1-1 atomic Structure: the nucleuS 3 42912_01_Ch01_0001-0027h.indd 3 1/10/14 11:40 AM Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

4 CHAPTER1 STRUCTURE AND BONDING of subatomic particles called neutrons.which are electrically neutral,and protons,which are positively charged.Because an atom is neutral overall,the number of positive protons in the nucleus and the number of negative elec- trons surrounding the nucleus are the same. Although extremely small-about 10-14 to 10-15 meter(m)in diameter- the nucleus nevertheless contains essentially all the mass of the atom.Elec trons have negligible mass and circulate around the nucleus at a distance of approximately 10-10 m.Thus,the diameter of a typical atom is about 2 X 10-10 m,or 200 picometers(pm),where 1 pm =10-12m.To give you an idea of how small this is,a thin pencil line is about 3 million carbon atoms wide.(Many organic chemists and biochemists,particularly those in the =100pm=10 this book.) FIGURE 13 Schematic view Nucleus(protons+neutrons an atom.The dense positively mass an view on the right shows calculated ectrons electron-density surfaces.Electror density ncrease A specific atom is described by its atomic number (Z),which gives the ater at the blue solid surface number of protons (or electrons)it contains.and its mass number (A).which than at the ra mesh surface. gives the total number of protons plus neutrons in its nucleus.All the atoms ofa given element have the same atomic number-1for hydrogen.6 for carbon 15 for phosphorus,and so on-but they can have different mass numbers depending on how many neutrons they contain.Atoms with the same atomic number but different mass numbers are called isotopes.The weighted average mass in unified atomic mass units(u)of an element's naturally occurring iso- topes is called the element's atomic weight-1.008 u for hydrogen,12.011 u for carbon,30.974 u for phosphorus,and so on. 12 Atomic Structure:Orbitals disi an atom ccording to the u del.the r of ed by a mathe sion c of ox th a fluid The P ation is called a wave function,or orbital,and is den oted by When the of the wave function 2 is plotted in three-dimensional space,an orbital describes the volume of sp ace around a nucleus that an elec tron is most likely to occupy.You might therefore think of an orbital as looking like a nhotog anh of the electron taken at a slow shutter sneed In such a photo,the orbital would ap pear as a blurry cloud,indicating the region of space around the nucleus where the electron has been.This electron cloud doesn't have a sharp boundary.but for practical purposes we can set the limits

of subatomic particles called neutrons, which are electrically neutral, and protons, which are positively charged. Because an atom is neutral overall, the number of positive protons in the nucleus and the number of negative electrons surrounding the nucleus are the same. Although extremely small—about 10214 to 10215 meter (m) in diameter— the nucleus nevertheless contains essentially all the mass of the atom. Electrons have negligible mass and circulate around the nucleus at a distance of approximately 10210 m. Thus, the diameter of a typical atom is about 2 3 10210 m, or 200 picometers (pm), where 1 pm 5 10212 m. To give you an idea of how small this is, a thin pencil line is about 3 million carbon atoms wide. (Many organic chemists and biochemists, particularly those in the United States, still use the unit angstrom (Å) to express atomic distances, where 1 Å 5 100 pm 5 10210 m, but we’ll stay with the SI unit picometer in this book.) Nucleus (protons + neutrons) Volume around nucleus occupied by orbiting electrons A specific atom is described by its atomic number (Z), which gives the number of protons (or electrons) it contains, and its mass number (A), which gives the total number of protons plus neutrons in its nucleus. All the atoms of a given element have the same atomic number—1 for hydrogen, 6 for carbon, 15 for phosphorus, and so on—but they can have different mass numbers depending on how many neutrons they contain. Atoms with the same atomic number but different mass numbers are called isotopes. The weighted average mass in unified atomic mass units (u) of an element’s naturally occurring isotopes is called the element’s atomic weight—1.008 u for hydrogen, 12.011 u for carbon, 30.974 u for phosphorus, and so on. 1-2 atomic Structure: orbitals How are the electrons distributed in an atom? According to the quantum mechanical model, the behavior of a specific electron in an atom can be described by a mathematical expression called a wave equation—the same sort of expression used to describe the motion of waves in a fluid. The solution to a wave equation is called a wave function, or orbital, and is denoted by the Greek letter psi, c. When the square of the wave function, c2, is plotted in three-dimensional space, an orbital describes the volume of space around a nucleus that an electron is most likely to occupy. You might therefore think of an orbital as looking like a photograph of the electron taken at a slow shutter speed. In such a photo, the orbital would appear as a blurry cloud, indicating the region of space around the nucleus where the electron has been. This electron cloud doesn’t have a sharp boundary, but for practical purposes we can set the limits FigUre 1.3 Schematic view of an atom. The dense, positively charged nucleus contains most of the atom’s mass and is surrounded by negatively charged electrons. The three-dimensional view on the right shows calculated electron-density surfaces. Electron density increases steadily toward the nucleus and is 40 times greater at the blue solid surface than at the gray mesh surface. Unless otherwise noted, all content on this page is © Cengage Learning. 4 chapter 1 Structure and Bonding 42912_01_Ch01_0001-0027h.indd 4 1/10/14 11:40 AM Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

by saying that an orbital represents the space where an electron spends 90% to 95% of its time. What do orbitals look like? There are four different kinds of orbitals, denoted s, p, d, and f, each with a different shape. Of the four, we’ll be concerned primarily with s and p orbitals because these are the most common in organic and biological chemistry. An s orbital is spherical, with the nucleus at its center; a p orbital is dumbbell-shaped; and four of the five d orbitals are cloverleaf-shaped, as shown in FigUre 1.4. The fifth d orbital is shaped like an elongated dumbbell with a doughnut around its middle. An s orbital A p orbital A d orbital The orbitals in an atom are organized into different layers around the nucleus, or electron shells, of successively larger size and energy. Different shells contain different numbers and kinds of orbitals, and each orbital within a shell can be occupied by a maximum of two electrons. The first shell contains only a single s orbital, denoted 1s, and thus holds only 2 electrons. The second shell contains one 2s orbital and three 2p orbitals and thus holds a total of 8 electrons. The third shell contains a 3s orbital, three 3p orbitals, and five 3d orbitals, for a total capacity of 18 electrons. These orbital groupings and their energy levels are shown in FigUre 1.5. 3rd shell (capacity—18 electrons) 2nd shell (capacity—8 electrons) 1st shell (capacity—2 electrons) Energy 3d 3p 2p 3s 2s 1s The three different p orbitals within a given shell are oriented in space along mutually perpendicular directions, denoted px, py, and pz. As shown in FigUre 1.6, the two lobes of each p orbital are separated by a region of zero electron density called a node. Furthermore, the two orbital regions separated by the node have different algebraic signs, 1 and 2, in the wave function, as represented by the different colors in Figure 1.6. As we’ll see in Section 1-11, the algebraic signs of the different orbital lobes have important consequences with respect to chemical bonding and chemical reactivity. FigUre 1.4 representations of s, p, and d orbitals. An s orbital is spherical, a p orbital is dumbbellshaped, and four of the five d orbitals are cloverleaf-shaped. Different lobes of p orbitals are often drawn for convenience as teardrops, but their true shape is more like that of a doorknob, as indicated. FigUre 1.5 energy levels of electrons in an atom. The first shell holds a maximum of 2 electrons in one 1s orbital; the second shell holds a maximum of 8 electrons in one 2s and three 2p orbitals; the third shell holds a maximum of 18 electrons in one 3s, three 3p, and five 3d orbitals; and so on. The two electrons in each orbital are represented by up and down arrows, hg. Although not shown, the energy level of the 4s orbital falls between 3p and 3d. Unless otherwise noted, all content on this page is © Cengage Learning. 1-2 atomic Structure: orBitalS 5 42912_01_Ch01_0001-0027h.indd 5 1/10/14 11:40 AM Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it

A 2px orbital A 2py orbital y A 2pz orbital y x y x z z z x 1-3 atomic Structure: electron Configurations The lowest-energy arrangement, or ground-state electron configuration, of an atom is a listing of the orbitals occupied by its electrons. We can predict this arrangement by following three rules: rule 1 The lowest-energy orbitals fill up first, according to the order 1s n 2s n 2p n 3s n 3p n 4s n 3d, a statement called the aufbau principle. Note that the 4s orbital lies between the 3p and 3d orbitals in energy. rule 2 Electrons act in some ways as if they were spinning around an axis, in somewhat the same way that the earth spins. This spin can have two orientations, denoted as up (h) and down (g). Only two electrons can occupy an orbital, and they must be of opposite spin, a statement called the Pauli exclusion principle. rule 3 If two or more empty orbitals of equal energy are available, one electron occupies each with spins parallel until all orbitals are half-full, a statement called Hund’s rule. Some examples of how these rules apply are shown in taBle 1.1. Hydrogen, for instance, has only one electron, which must occupy the lowest-energy orbital. Thus, hydrogen has a 1s ground-state configuration. Carbon has six electrons and the ground-state configuration 1s2 2s2 2px 1 2py 1, and so forth. Note that a superscript is used to represent the number of electrons in a particular orbital. taBle 1.1 ground-State electron Configurations of Some elements Element Atomic number Configuration Element Atomic number Configuration Hydrogen 1 1s Phosphorus 15 3s 2s 1s 3p Carbon 6 2p 2s 1s 2p FigUre 1.6 Shapes of the 2p orbitals. Each of the three mutually perpendicular, dumbbellshaped orbitals has two lobes separated by a node. The two lobes have different algebraic signs in the corresponding wave function, as indicated by the different colors. Unless otherwise noted, all content on this page is © Cengage Learning. 6 chapter 1 Structure and Bonding 42912_01_Ch01_0001-0027h.indd 6 1/10/14 11:40 AM Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it