Structures and Bonding

2 Standard Enthalpies of Formation of the Small Chalcogen Clusters E (n = 1-8) 

Important thermodynamic properties that relate to the structure and stability of the chalcogen ailotropes and their polyatomic cations are the formation enthalpies listed in Table 2. Only reliable experimentally or quantum chemically established numbers have been included. From Table 2 it is evident that tellurium is the least investigated with respect to the entries thus, there is clearly space for more thorough experimental or quantum chemical work in this direction. Therefore, we have assessed the missing Te data from the IP determination in ref. 12 (PE spectroscopy) and ref. 13 (quantum chemical calculations) and have put them in the table in parentheses, although it is clear that the associated error bars are relatively high. The data in ref. 14 were not considered. 

Note Values in bold are from the NIST,15 values in parentheses have been put together by the author from PE-spectroscopy data12 of Te and Te calculations (n = 1-6).13 

Structure and Bonding of the Neutral Chalcogens and their Polyatomic Cations 

1 One phosphorus and three chlorine atoms supply 5 + (3 x 7) = 26 valence electrons. Since P is less electronegative than Cl, it is likely to be the central atom, so the 13 pairs of electrons are distributed as shown below. In this case, each atom obeys the octet rule, Whenever it is possible to follow the octet rule without violating other electron counting rules, you should do so. 

2 The Lewis structures and the shapes of HjS, XeO4, and SOF4 are shown below. According to the VSEPR model, electrons in bonds and in lone pairs can be thought of as charge clouds that repel one another and stay as far apart as possible. First, write a Lewis structure for the molecule, and then arrange the lone pairs and atoms around the central atom, such that the lone pairs are as far away from each other as possible. 

3 The Lewis structures and molecular shapes for XcFi and ICb are shown below. The XeFi Lewis structure has an octet for the 4 F atoms and an expanded valence shell of 10 electrons for the Xe atom, with the 8 + (2 x 7) = 22 valence electrons provided by the three atoms. The five electron pairs around the central Xe atom will anange themselves at the comers of a trigonal bipyramid (as in PF5). The three lone pairs will be in the equatorial plane, to minimize lone pair-lone pair repulsions. The resulting shape of the molecule, shown at the right, is linear (i.e., the F-Xe-F bond angle is 180°). 

Two chlorine atoms and one iodine atom in total have 21 electrons. However, we have a cationic species at hand, so we have to remove one electron and start with a total of 20 valence electrons for ICI2. That gives a Lewis structure in which iodine is a central atom (being the more electropositive of the two) and is bonded to two chlorines with a single bond to each. All atoms have a precise octet. Looking at iodine, there are two bonding 

If we add one electron to O2 we obtain the next species, anion O . This extra electron continues to fill 1 Jig level but it has to have an antiparallel spin with respect to already present electron. Thus, after O2 molecule receives an electron, one electron pair is formed and only one unpaired electron is left. 

The general rule of bonding Atoms strive to attain a complete outer shell of valence electrons (Section 1.2). H wants 2 electrons. Second-row elements want 8 electrons. 

Formal charge (FC) is the difference between the number of valence electrons of an atom and the number of electrons it owns (Section 1.3C). See Sample Problem 1.4 for a stepwise example. 

Curved arrow notation shows the movement of an electron pair. The tail of the arrow always begins at an electron pair, either in a bond or a lone pair. The head points to where the electron pair moves (Section 1.5). 

Electrostatic potential plots are color-coded maps of electron density, indicating electron rich and electron deficient regions (Section 1.11). 

A properly drawn Lewis structure shows the number of bonds and lone pairs present around each atom in a molecule. In a valid Lewis structure, each H has two electrons, and each second-row element has no more than eight. This is the first step needed to determine many properties of a molecule. 

Online homework for this and other chapteis may be assigned in Organic OWL. 

Friediich Wohler (1800-1882) was born in Eschersheim, Germany, and studied at Heidel berg under Leopold Gmelin. From 1836 to 1882, he was professor of chemistry at Gottingen. Wohler developed tho first industrial method for preparing aluminum metal, and he discovered several new elements In addition, he wrote textbooks about both inorganic and organic chemistry. 

Little more than a decade later, the vitalistic theorv suffered still further when Friedrich Wohler discovered in 1828 that it was possible to convert the inorganic salt ammonium cyanate into the organic substance urea, which had previously been found in human urine. 

The valence-bond pictures for an isocyanide and carbon monoxide, and for metal complexes of these ligands, emphasize the similarities of both the ligands and their complexes. 

This simple picture of bonding is convenient to use, and often completely acceptable. However, it does lack sophistication and may not be used to explain some of the subtleties of these systems. One obvious point in this regard concerns infrared spectral data. Coordination of carbon monoxide to a metal invariably leads to a lower carbonyl stretching frequency (vco). implying a lower CO bond order as predicted. However, the values for vcn may be considerably higher for metal complexes of an isocyanide than are the values for the ligand itself. The valence-bond picture cannot rationalize 

The valence-bond picture does not adequately express a difference between various isocyanides. There are interesting differences between alkyl and aryl isocyanides, discussed below. 

Incidentally, isocyanides are polar (for CNC H, the dipole moment is 3.44 D) and they are good bases (vs. BRj, H+), whereas CO is a poor base hence isocyanides can function as ligands in metal complexes where carbon monoxide does not. The scarcity of low-valent isocyanide complexes is less easily explained, however. Arguments involving 77-acceptor capacity are quite inappropriate. More data on low-valent species, and evaluations of stabilities, modes of decomposition, and reactions are desirable. 

A simple molecular orbital picture (using, e.g., an species for 

The magnesium dialkyls are colourless solids, which react readily with oxygen and water and which usually decompose without melting at high temperatures. The pathways followed in their thermal decomposition are typical of many alkyl derivatives of main group and of transition elements. Where a ( -C—H is present, as in Et Mg, jS-hydrogen transfer predominates with loss of alkene  

Donor solvents tend to break down the polymers by coordination to the Lewis 

The highly polar character of organolithium compounds causes strong association. The geometry of the coordination sphere is determined essentially by steric effects, as in ionic structures, rather than by interaction of electron pairs. Even where lithium may appear to possess an octet configuration, it is not envisaged that the electrons are strongly held by the valence orbitals of the metal in covalent bonds. 

Crystalline methyllithium consists of tetrameric aggregates (Fig. 3.4). Each carbon atom is bound to three hydrogen atoms and is equidistant from the three lithium atoms which are at the corners of a triangular face of the Li4 tetrahedron. The formal coordination number of carbon is therefore seven. The structure consists of two interpenetrating and unequal tetrahedra, one Li and one C. The Li C skeleton can thus be represented as a distorted cube. The methyl carbon of one tetramer is only 2.36 A from a lithium atom of a neighbouring tetramer. This interaction makes methyllithium involatile and sparingly soluble in hydrocarbons. v 

There are also tetramer units (EtLi) in crystalline ethyllithium, although they associate in linear fashion rather than in three dimensions. These tetrameric clusters are retained in complexes of alkyl and aryllithiums with donor molecules. 

Cresswell, W. T., Leicester, J., Bond Refractions for Tin, Silicon, Lead, Germanium and Mercury Compounds, J. Phys. Chem. 58 [1954] 174/7. 

Dissociation Energies of Metal-Carbon Bonds and the Excitation Energies of Metal Atoms in Combination, Pure Appl. Chem. 2 [1961] 61/9. 

Skinner, H. A., The Strength of Metal-to-Carbon Bonds, Advan. Organometal. Chem. 2 [1964] 49/114. 

Kuzman-Borbely, A., Palossy-Becker, K., Bond Structure in the Aryl Derivatives of the Elements of Group IV, J. Organometal. Chem. 7 [1967] 393/404. 

Aylett, B. J., The Stereochemistry of Main Group IV Elements, Progr. Stereochem. 4 [1969] 213/71. 

In the previous section we have developed a geometric system that can be used to represent the structure of actual crystals. In the simplest actual crystal, the atoms coincide with the points of one of the Bravais lattices. Examples include chromium, molybdenum, 

Most organic species form molecular crystals in which discrete molecules are arranged in fixed positions relative to the lattice points. This of course means that the individual atoms making up the molecules are each arranged at fixed positions relative to each other, the lattice point, and the other molecules. The forces between molecules in molecular crystals are generally weak when compared with the forces within a molecule. The structure of molecular crystals is affected by both the intermolecular forces and the intramolecular forces since the shapes of the individual molecules will affect the way the molecules pack together. In addition, the properties of the individual molecule, such as the polarity, will affect the intermolecular forces. The forces between the molecules in molecular crystals include electrostatic interactions between dipoles, dispersion forces, and hydrogen bond 

Bragg s law shows us that, if x-rays of a known wavelength are used and the incident angle of the radiation is measured, determination of the interplanar spacing of a crystal is possible. This is the foundation of x-ray diffraction methods that are used to analyze or determine the structure of crystals. Several different experimental methods making use of x-ray diffraction and Bragg s law have been developed and are used depending on the type of sample that is available and the information desired. 

The most powerful method that can be used to determine unknown crystal structures is the rotating crystal technique. In this method a single crystal of good quality (of at least 0.1 mm in the smallest dimension) is mounted with one of its axes normal to a monochromatic beam of x-rays and rotated about in a particular direction. The crystal is surrounded by cylindrical film with the axis of the film being the same as the axis of rotation of the crystal. By repeating this process of rotation in a number of directions, the rotating crystal method can be used to determine an unknown crystal structure. 

It is unlikely that you will ever need to use the rotating crystal method to determine an unknown structure since most materials you are likely to crystallize have structures that have been determined. This will not be true for a newly developed compound, and is rarely true for proteins and other biological macromolecules. 

When a carboxyl group is attached to a ring, the parent ring is named (retaining the final -e) and the suffix -carboxylic acid is added, as shown in entries 9 and 10. 

Compounds with two carboxyl groups, as illustrated by entries 11 through 13, are distinguished by the suffix -dioic acid or -dicarboxylic acid as appropriate. The final -e in the name of the parent alkane is retained. 

The list of carboxylic acids in Table 18.1 is by no means exhaustive insofar as common names are concerned. Many others are known by their common names, a few of which follow. Give a systematic lUPAC name for each. 

Sample Solution (a) Methacrylic acid is an industrial chemical used in the preparation of transparent plastics such as Lucite and Plexiglas. The carbon chain that includes both the carboxylic acid and the double bond is three carbon atoms in length. The compound is named as a derivative of propenoic acid. The preferred 2004 lUPAC name, 2-methylprop-2-enoic acid, contains locants for both the methyl group and the double bond. Older, but still permissible, lUPAC names omitted the double-bond locant because only one position for the double bond is structurally possible. 

The Structural features of the carboxyl group are most apparent in formic acid, which is planar, with one of its carbon-oxygen bonds shorter than the other, and with bond angles at carbon close to 120°. 

The photoelectron spectra (PES) of several neutral bisarene-metal complexes have been obtained (Table I) and the spectra assigned on the basis of a simple MO model 110, 111). An energy level diagram was deduced and is shown in Fig. 1. The predominantly ring e and ejg 

Photoelectron Spectra of Some Bisarene-Metal Complexes 

Compound or cation No. of unpaired electrons fi eff Exptl. (BM) fi eff Spin only (BM) References 

The observed experimental ionization energies for the bisarene complexes are in reasonable agreement with detailed MO calculations 8, 95, 372). 

Mass spectral studies on bisarene chromium derivatives have shown that the strength of the metal arene bond increases when electron- 

9 kcal mol for Ru—N bond rotation. Thus, increasing electron density at the metal corresponds to lower Ru—N barrier and an increased N—C barrier. These considerations and the use of these complexes for the activation of H—H bonds or species with non-polar C—H bonds have been discussed by Gunnoe,  

Insight into the nature of the chemical bond has been intensively developed since the publication of Pauling s famous first review. Frenking and Shaik gave a more recent review. More details can be found in Kittel s classical treatment of solid state physics. 

Thomson Throughout this chapter, there are opportunities for online self-study, linking you to interactive tutorials based on your level of understanding. Sign in at www.thomsonedu.com to view organic chemistry tutorials and simulations, develop problem-solving skills, and test your knowledge with these interactive self-study resources. 

Although the drawings may appear unintelligible at this point, don t worry. Before long they ll make perfectly good sense and you ll be drawing similar structures for any substance you re interested in. 

This suggests sp hybridization at carbon, and a ct + tt carbon-oxygen double bond analogous to that of aldehydes and ketones. 

Carboxylic acids are fairly polar, and simple ones such as acetic acid, propanoic acid, and benzoic acid have dipole moments in the range 1.7-1.9 D. 

The melting points and boiling points of carboxylic acids are higher than those of hydrocarbons and oxygen-containing organic compounds of comparable size and shape and indicate strong intermolecular attractive forces. 

Hydrogen bonding between two acetic acid moiecuies. 

Additionally, sp hybridization of the hydroxyl oxygen allows one of its unshared electron pairs to be delocalized by orbital overlap with the tt system of the carbonyl gronp (Fignre 19.1). In resonance terms, this electron delocalization is represented as  

Lone-pair donation from the hydroxyl oxygen makes the carbonyl gronp less electrophilic than that of an aldehyde or ketone. The graphic that opened this chapter is an electrostatic potential map of formic acid that shows the most electron-rich site to be the oxygen of the carbonyl group and the most electron-poor one to be, as expected, the OH proton. 

Results of such investigations suggest that there are four limiting kinds of structure and these will be briefly considered. 

In a pure metal the atoms of the solid are arranged in closely packed layers. There is more than one way of achieving close packing but it 

This is one of the most familiar types of structure in inorganic chemistry. The crystals can usually be melted in the laboratory 

In substances which are liquid or gaseous at ordinary temperature, the forces of attraction between the particles are so weak that thermal vibration is sufficient for them to be broken. These substances can be converted into solids by cooling to reduce the thermal energy. 

The above classification of structures is made primarily for convenience. In fact, the structures of many compounds cannot be precisely described under any of these classes, which represent limiting, or ideal cases. However, we shall use these classes to examine further the limiting types of bonding found in them. 

All borabenzene-metal complexes investigated structurally so far show very similar patterns for the ligand geometry (Table I) and for the metal-ligand bonding (Table II) only the cobalt complex 6 deserves separate consideration (see below). 

In bonding to the ligand the metal is always shifted away from the boron and interacts most strongly with C-4. This slip distortion is larger than expected considering the difference between the covalent radii of boron and carbon alone (22), and thus must partially be of electronic origin (cf. refs. 36 and 37). 

The bonding situation in borabenzene-metal complexes has been treated by several authors and with varying methods and intentions (38-41). The complexes are partitioned in boratabenzene ions and positive complex fragments or metal ions. The tt MO s of the C5H5BR ligand (Fig. 2) may 

Qualitative tt MO s of the C5H5BR ligand in comparison with the C6H6 and Cp 

The above results justify a simple ligand field model for the bis(ligand) metal species which is based on the assumption of pseudoaxial symmetry (40). This model allowed a consistent reinterpretation of an early ESR study of Co(C5H5BPh)2 (13) (42) the reinterpretation was later confirmed by additional and more sophisticated ESR work on 13 (43,44). 

The preferred tetravalence may be explained with the hybridization model the energetic difference between 2s- and 2p-orbitals is rather low compared to the energy released in chemical bonding. Therefore, it is possible for the wavefunc- 

Before examining organic molecules in detail, we must review some important features about structure and bonding learned in previous chemistry courses. We wiU discuss these concepts primarily from an organic chemist s perspective, and spend time on only the particulars needed to understand organic compounds. 

Important topics in Chapter 1 include drawing Lewis stractures, predicting the shape of molecules, determining what orbitals are used to form bonds, and how electronegativity affects bond polarity. Equally important is Section 1.7 on drawing organic molecules, both shorthand methods routinely used for simple and complex compounds, as weU as three-dimensional representations that allow us to more clearly visuahze them. 

All matter is composed of the same building blocks called atoms. There are two main components of an atom. 

Th i ge a proton is equ in magnitu but opposite in sign to the charge on an electron. In a neutral atom, the number of protons in the nucleus equals the number of electrons. This quantity, called the atomic number, is unique to a particular element. For example, every neutral carbon atom has an atomic number of six, meaning it has six protons in its nucleus and six electrons surrounding the nucleus. 

In addition to neutral atoms, we will also encounter charged ions. 

also known as dinitrogen oxide, is a colorless gas with a sweet odor and taste. The molecule has a linear geometry as predicted with simple valence shell electron pair repulsion (VSEPR) theory. Formal charge considerations suggest that the most important two resonance structures are  

The N-N and N-O bond lengths determined from rotational spectroscopy measurements are 1.128 and 1.184 A, respectively [170-172]. The N-N bond is 

having N and O heteroatoms which may normally serve as good ligands to metal ions, might be expected to have ligating properties somewhat similar to those of dinitrogen or NO. However, N2O coordination complex adducts reported in the literature are extremely scarce. Actually, only one reasonably well characterized N2O coordination complex is known up to this day, i.e. that reported and studied by Armor and Taube [173-175]. Spectral evidence suggests the existence of [Ru(NH3)5(N20)j which is in equilibrium with N2O in the reaction of N2O plus [Ru(NH3)5(H20)]. Diamantis and Sparrow soon thereafter isolated this complex in microcrystaUine solid forms, and obtained analytical and spectroscopic data consistent with the proposed formulation [176-179]. 

When N2O is bonded through the terminal N-atom, the Ru -N-N-0 unit is linear however, ruthenium ligation to the O-atom leads to a predicted strongly bent structure with ZRu-0-N-N=138°. 

The researchers noted that the theoretical model of the end-on terminal binding through the N (rather than 0)-atom is more consistent with the experimental spectroscopic data mode. The studies also revealed that Ru -N20 bond is dominated by 7i back-donation, which, however, is weak compared to that found in the corresponding known ruthenium-nitrosyl complex. See further discussions below for possible bridge binding of N2O in a copper enzyme. 

Some recent additions to the series of doubly bonded Group 14 species also include the unusual compounds [L - E = E - L] [E = Si, Ge L = C(NDippCH)2] (53) which contain the dimeric Ej unit with both tetrel atoms in the zero oxidation state, stabilized by Af-heterocydic carbene donor groups. The small L-Si=Si angles in the silicon derivative (93.4°) imply a high degree of p-orbital involvement in bonding, with minimal contributions from s electrons, which remain localized at the E centers [71, 79]. 

The description of the bond order within the Group 14 alkyne analogs is even more contentious than those of the doubly bonded derivatives. It is only fairly recently that the series of REER species has been prepared and characterized. They are valence-isoelectronic with the triply bonded dianion [Ar 2Ga2] (54) (Ar = 2,6-Dipp-CgH, ) first synthesized by Robinson [83], which provoked vigorous 

Capsaicin is the compound responsible for the characteristic spicy flavor of jalapeho and habahero peppers. Although it first produces a burning sensation on contact with the mouth or skin, repeated application desensitizes the area to pain. This property has made it the active ingredient in several topical creams for treatment of chronic pain. Capsaicin has also been used as an animal deterrent in pepper sprays, and as an additive to make birdseed squirrel-proof In Chapter 1, we discuss the structure, bonding, and properties of organic molecules like capsaicin. 

The charge on a proton is equal in magnitude but opposite in sign to the charge on an electron. In a neutral atom, the number of protons in the nucleus equals the number of electrons. 

In all compounds, with the exception of the bis(allyl) complex 57, an almost linear arrangement P—Pd—Pd—P is found. In 57, the angle Pd—Pd—P deviates significantly from 180°, being 127.4° (25). 

The Pd—Pd bond length lies between 2.61 A (for 84) and 2.72 A (for 57), varying surprisingly little for the different types of bridging ligands. This relatively short distance, comparable with the interatomic distance in metallic palladium (2.74 A), points to the existence of a direct metal-metal bond. 

The distances Pdl-C6 and Pd2-C8 in the /x-allyl complexes 8, 21, 56,57 lie between 2.10 and 2.20 A and, therefore, do not differ from those between the palladium atoms Pdl and Pd2 and the carbon atoms Cl and C3 of the C5H5 ring. 

By optimizing the orientation of the (Y)M2L2+ unit below the plane of the C5H5 ring, the calculations also show that the barrier for a hapto-tropic shift (34) according to the process 

Atoms consist of a dense, positively charged nucleus surrounded by negatively charged electrons. 

The atomic number (Z) gives the number of protons in the nucleus. 

The mass number (A) gives the total number of protons and neutrons. 

All atoms of a given element have the same value of Z. 

The distribution of electrons in an atom can be described by a wave equation. 

Figute1.2 Boronic acid derivatives analyzed by X-ray crystallography. 

Due to electronegativity differences (B = 2.05, C = 2.55) and notwithstanding the electronic deficiency of boron, which is mitigated by the two electron-donating oxygen atoms (vide supra), the inductive effect of a boronate group should be that of a weak electron-donor. The NM R alpha effect of a boronate group is very small [27]. 

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. 

Why This Chapter We ll ease into the study of organic chemistry by first reviewing some ideas about atoms, bonds, and molecular geometry that you may recall from yoirr general chemistry course. Much of the material in this chapter and the next is likely to be familiar to you, but it s nevertheless a good idea to make sure you understand it before going on. 

Note that an indirect-gap semiconductor is impossible in an amorphous material as crystalline directions for indirect minima are undefined. Therefore, all amorphous semiconductors have direct gaps. 

Finally, the fourth type of state is the non-bonding dangling bond. Dangling bonds have energies near the middle of the gap where non-bonding states would be 

It is possible to produce some amorphous compound semiconductors such as amorphous GaAs. These materials have a distinction between dangling bonds associated with the cation and the anion. Therefore, non-bonding states of type (4) would not necessarily he at or near the middle of the mobility gap. In principle, H passivation of such states is also possible. These materials are generally less stable and less homogeneous in amorphous form than other amorphous materials and are not widely used in technology apphcations. 

One can also consider hydrogen as effectively an alloying element. It has been found, for example, that the mobility gap is directly related to the H2 pressure in the 

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Madey T E 1986 Electron- and photon-stimulated desorption probes of structure and bonding at surfaces Science 234 316... 

STRUCTURE AND BONDING 39 The basic tetrahedral shape is even more distorted producing an... 

Chemical Reviews Chemical Society Reviews Structure and Bonding... 

Structure and Bonding in Noncrystalline Solids G. E. Walrafen, A. G. Revesz, Eds., Plenum, New York (1986). 

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