Organic Chemistry Notes (UPMC, Licence Chimie, LC 204) Introduction The Chemical Bond: a revision. Quantum Shells (1, 2, 3, 4, 5) and Sub-Orbitals (s, p, d, f) Electrons in atoms arrange themselves in the quantum shells in groups of 2, 8, 8, 18, etc. There are four types of orbitals (also called sub-levels), s, p, d, and f, which bear different shapes, each one being able to host up to two electrons. 1st Quantum Shell contains 2 electrons 1s (x 1) 2 electrons 2nd Quantum Shell contains 8 electrons 2s (x 1) 2 electrons 2p (x 3) 6 electrons 3rd Quantum Shell contains 8 electrons 3s (x 1) 2 electrons 3p (x 3) 6 electrons 4th Quantum Shell contains 18 electrons 4s (x 1) 2 electrons 3d (x 5) 10 electrons 4p (x 3) 6 electrons 5th Quantum Shell contains 18 electrons 5s (x 1) 2 electrons 4d (x 5) 10 electrons 5p (x 3) 6 electrons 1 Table 1. Ground state electron configuration in elements Atomic Number Symbol 1 2 3 4 5 6 7 8 9 10 11 H He Li Be B C N O F Ne Na Configuration 1s1 1s2 1s2 2s1 1s2 2s2 1s2 2s2 2p1 1s2 2s2 2p2 1s2 2s2 2p3 1s2 2s2 2p4 1s2 2s2 2p5 1s2 2s2 2p6 [Ne] 3s1 15 16 17 18 P S Cl Ar [Ne] [Ne] [Ne] [Ne] 3s2 3s2 3s2 3s2 3p3 3p4 3p5 3p6 Figure 1 The Periodic Table The chemical elements are gathered in a tabular way in a periodic table, which brings together the peculiar features of each element. Several conceptually and graphically different representation of the periodic table have been reported over the years since the first conception, by Dmitri Mendeleev. Here below a modern representation of the periodic table showing the different "families" of the elements. All the elements of a particular family share common features. Each line is called period and each column is called group and both are numbered (1, 2, 3….) (Figure 2). Figure 2 The covalent bond 1 The closed shell configuration represents a particularly favorable situation and may be reached when two neighboring atoms share electrons from their outermost shell. So, for example, when two neighboring chlorine atoms share each one electron from their outer (valence) shell, we have a stable dichlorine molecule, featuring a covalent bond between the two chlorine atoms. For clarity sake, when writing a molecule structure, we normally explicit only the electrons involved in the bond between the atoms, and, sometimes, those of the outer shell. Electrons may be symbolized either with dots or dashes (Lewis notation). Explicit illustration of the outer shell electrons in an organic chemistry course is highly recommended, as it allows to clearly locating the electron flow in a (ionic) chemical reaction. 1 Lower, S. http://www.chem1.com/acad/webtext/chembond/cb03.html 2 Dichlorine electrons of the outermost sphere shared electron pair 1 (s 2) 2 (s 2,p 6) Cl .. .....Cl......Cl... Cl Cl Cl Cl 3 (s2 ,p 5) Cl-Cl simplified notations dichlorine molecule chlorine atom Cl-Cl Figure 3 The number of electrons composing the stable closed shell depends on the quantum shell considered. Period 1: s2, period 2: 2s22p6 (octet), period 3: 3s23p6 (octet) or more 3s23p63dn (expanded octet). This (expanded octet) situation may occur in atoms such as Si, P, S, Cl, whose d orbitals are energetically close to the most highlyoccupied s2p6 orbitals that they can become involved in electron-sharing with other atoms. As a result, they can bond to more than four atoms, and thus need to involve more than the four pairs of electrons available in an s2p6 octet. Some example are described here below: (Figure 4: LiH; Figure 5: PCl3), Figure 6: PCl5). Lithium hydride 2 electrons in the outermost sphere for each atoms 1s Li H Li H lithium hydride Figure 4 Phosphorous trichloride Cl 8 electrons in the outer sphere of P in 3s and 3p orbitals (octet). 5 electrons belonging to P, of which 3 shared with 3 Cl (each Cl sharing in turn one electron) plus 2 electrons as a non-bonding lone pair. 8 electrons in the outer sphere of each Cl in 3s and 3p orbitals (octet). 7 electrons belonging to each Cl of which 1 shared with P P P Cl Cl Cl Cl Cl phosphorous trichloride P: 1s 2 // 2s2 2p6 // 3s 2 3p 3 Cl:1s 2 // 2s2 2p6 // 3s 2 3p 5 Figure 5 3 Phosphorous pentachloride 10 electrons in the outer sphere of P in 3s, 3p, and 3d orbitals (expanded octet). 5 electrons belonging to P, all shared with the five Cl's. 8 electrons in the outer sphere of each Cl in 3s and 3p orbitals (octet) Cl 7 electrons belonging to each Cl of which 1 shared with P Cl Cl Cl Cl P P Cl Cl Cl Cl phosphorous pentachloride Cl P: 1s 2 // 2s2 2p6 // 3s 2 3p 3 Cl:1s 2 // 2s2 2p6 // 3s 2 3p 5 Figure 6 Building a correct Lewis structure for a molecule Knowing the above "rules" of the covalent bonding between atoms, we can now, given a raw formula of an unknown molecule, try to play with the outer sphere electrons of the composing atoms, to locate the covalent bonds, and therefore the connectivity ( Figure 7). H duet C N O F P S Cl Br octet octet or expanded octet I Figure 7 4 Accordingly, we can now build up, although in a rather raw way, the valence bonds for simple organic molecules such as methane, ethane, ethylene, and acetylene (Figure 8). H 1 CH4 C 4 H H C H H H C H H methane C2 H 6 2 H H 1s 1 C 1s 2 2s 2 2p2 6 C C 1s2 2s 2 2p 2 H H H 1s1 H H C C H H H H H C C H H H H ethane 2nd C-C bond () H H C2 H 4 4 C 2 C H H H C C C H H H H ethylene H 1s 1 C 1s 2 2s2 2p2 1 st C-C bond ( 2 nd C-C bond ( ) C 2H 2 2 2 C C H H C H H C C H acetylene 2 2 C 1s 2s 2p 2 H 1s 1 3 rd C-C bond ( ) 1 st C-C bond ( Figure 8 The shapes of the orbitals and the multiple bonds So far we have treated atomic orbitals as undifferentiated "little balls". However, such regions of space having the highest probability to host (up to two) electrons posses well defined geometries. More precisely, whereas s orbitals feature a spherical geometry, p atomic orbitals are directed toward the Cartesian axes and bear a rabbit-like shape (Figure 9). z z x x y s z z y px x y py x y pz Figure 9 With this information we can now start building up very simple organic molecules, appreciate the geometry of the atoms involved, and understand the notion of multiple bond. 5 Let's take first a hydrogen atom and its lone electron in its 1s atomic orbital (Figure 10, top). Now, consider a carbon atom. Its outermost 2nd quantum shell contains four electrons: two electrons in the 2s orbital and two electrons in two singly occupied p orbitals (Figure 10, bottom, A). Now, imagine to promote one of the electrons of the doubly filled 2s level into the empty p orbital (Figure 10, bottom, B). The appropriate combination of these four singly occupied orbitals (1s and 3p) gives rise to four identical orbitals directed along a tetrahedron: the so called sp3 hybridation (Figure 10, bottom, C). H 1s1 C 2s1 2p2 2s2 A 2p 3 4e - sp 3 B C Figure 10 If we now take four of the above described hydrogen atoms and move them toward the fours lobes of the sp3 hybrid of the carbon atom we "create" fours C-H bonds. We have "created" methane! Figure 11. H + 1s 1 1s1 1s 1 1s H H H 1 4e- sp3 Figure 11 Let's now start again from a carbon atom, and proceed as in Figure 10 until stage B. However, now we combine in the hybridization process just three of the fours orbitals, leaving the p z atomic orbital untouched, we create an sp2 hybrid for carbon atom (Figure 12). Such a hybrid has a trigonal (planar) geometry. z z x C y y 2p2 2s 2 z x 2s 1 A 2p3 B 4e - sp2 C Figure 12 If we now combine two such C atoms via interpenetration of two sp2 lobes and "add" four hydrogen atoms to the remaining four sp2 lobes we are on the edge of creating ethylene. However, for the moment we have built only the single C-C bond. Interaction between the two unused pz orbitals of each C atom generates a second CC bond. Thus, ethylene features a double C=C bond. As we can see, the two carbon bonds are different. The first one is the result of a combination of the sp2 hybridized lobes, whereas the second results from the 6 interaction of the two parallel pz atomic orbitals. The former CC bond is stronger and is defined a - bond, whereas the latter is weaker and is known as a -bond (Figure 13).2 -bond H H C C H H -bond Figure 13 If we now repeat the process of Figure 10 until stage B combining in the hybridization process just one s and and one p, we create an sp hybrid for carbon atom (Figure 14). Such a hybrid has a linear geometry. In this case the remaining unused p orbitals are two; py and pz. z z x x C y y 2s 1 2p2 2s 2 z A y 4e - sp 2p3 B C Figure 14 Now, combining two such C atoms via their sp lobes and adding two hydrogen atoms to the remaining two sp lobes we can create the σ bonds of acetylene. Interaction between the two unused pz orbitals of each C atom and, similarly, between the two unused py orbitals, generates two mutually orthogonal π-type CC bonds. Thus, acetylene has a CC triple bond (Figure 15)! -bond z z H C C H y y -bond Figure 15 2 A -bond is a bond whose orbital does not change of sign upon rotation of 180° around the bond axis, whereas a -bond does. 7