Molecular shape atoms

On the assumption that the pairs of electrons in the valency shell of a bonded atom in a molecule are arranged in a definite way which depends on the number of electron pairs (coordination number), the geometrical arrangement or shape of molecules may be predicted. A multiple bond is regarded as equivalent to a single bond as far as molecular shape is concerned. 

Given the diversity of different SCRF models, and the fact that solvation energies in water may range from a few kcal/mol for say ethane to perhaps 100 kcal/mol for an ion, it is difficult to evaluate just how accurately continuum methods may in principle be able to represent solvation. It seems clear, however, that molecular shaped cavities must be employed, the electiostatic polarization needs a description either in terms of atomic charges or quite high-order multipoles, and cavity and dispersion terms must be included. Properly parameterized, such models appear to be able to give absolute values with an accuracy of a few kcal/mol." Molecular properties are in many cases also sensitive to the environment, but a detailed discussion of this is outside the scope of this book. ... 

Valence, 286 Valence electrons, 269 and ionization energies, 269 Vanadium atomic radius, 399 eleciron configuration, 389 oxidation numbers, 391 pentoxide catalyst, 227 properties, 400, 401 van der Waals forces, 301 elements that form molecular crystals using, 301 and molecular shape, 307 and molecular size, 307 and molecular substances, 306 and number of electrons, 306 van der Waals radius, 354 halogens, 354 Vanillin, 345... 

As outlined in Section III.A, knowledge of the molecular wavefunction implies knowledge of the electron distribution. By setting a threshold value for this function, the molecular boundaries can be established, and the path is open to a definition of molecular shape. A quicker, but quite effective, approach to this entity is taken by assuming that each atom in a molecule contributes an electron sphere, and that the overall shape of a molecular object results from interpenetration of these spheres. The necessary radii can be obtained by working backwards from the results of MO calculations21, or from some kind of empirical fitting22. 

The quasi-classical theory of spectral shape is justified for sufficiently high pressures, when the rotational structure is not resolved. For isotropic Raman spectra the corresponding criterion is given by inequality (3.2). At lower pressures the well-resolved rotational components are related to the quantum number j of quantized angular momentum. At very low pressure each of the components may be considered separately and its broadening is qualitatively the same as of any other isolated line in molecular or atomic spectroscopy. 

The next most important aspect of a molecular compound is its shape. The pictorial representations of molecules that most accurately show their shapes are images based on computation or software that represents atoms by spheres of various sizes. An example is the space-filling model of an ethanol molecule shown in Fig. C.2a. The atoms are represented by colored spheres (they are not the actual colors of the atoms) that fit into one another. Another representation of the same molecule, called a ball-and-stick model, is shown in Fig. C.2b. Each ball represents the location of an atom, and the sticks represent the bonds. Although this kind of model does not represent the actual molecular shape as well as a space-filling model does, it shows bond lengths and angles more clearly. It is also easier to draw and interpret. 

In this section, we construct a model of molecular shape empirically, which means that we base it on rules suggested by experimental observations rather than on more fundamental principles. We proceed in three steps. First, we set up the basic nodel for simple molecules without lone pairs on the central atom. Then, we elude the effects of lone pairs. Finally, we explore some of the consequences of ecular shape. 

The Lewis structures encountered in Chapter 2 are two-dimensional representations of the links between atoms—their connectivity—and except in the simplest cases do not depict the arrangement of atoms in space. The valence-shell electron-pair repulsion model (VSEPR model) extends Lewis s theory of bonding to account for molecular shapes by adding rules that account for bond angles. The model starts from the idea that because electrons repel one another, the shapes of simple molecules correspond to arrangements in which pairs of bonding electrons lie as far apart as possible. Specifically ... 

Once we have identified the arrangement of the most distant locations of these regions, which is called the electron arrangement of the molecule, we note where the atoms lie and identify the shape of the molecule by giving it the name of the corresponding shape in Fig. 3.1. In naming the molecular shape, we consider only the positions of atoms, not any lone pairs that may be present on the central atom, even though they affect the shape. 

STRATEGY For the electron arrangement, draw the Fewis structure and then use the VSEPR model to decide how the bonding pairs and lone pairs are arranged around the central (nitrogen) atom (consult Fig. 3.2 if necessary). Identify the molecular shape from the layout of atoms, as in Fig. 3.1. 

Step 3 Locate the atoms and identify the molecular shape (according to Fig. 3.1). 

Self-Test 3.8A Describe (a) the electron arrangement, (b) the molecular shape, and (c) the hybridization of the central chlorine atom in chlorine trifluoride. 

Molecules and ions, like atoms, can be isoelectronic. That is, they can have the same number of electrons. For example, CH4 and NH4+ are isoelectronic. Therefore, they have the same molecular shape. Identify a molecule or ion that is isoelectronic with each of the following species and verify that each pair has the same shape (a) CO 2 (b) 0 ... 

With the development of accurate computational methods for generating 3D conformations of chemical structures, QSAR approaches that employ 3D descriptors have been developed to address the problems of 2D QSAR techniques, that is, their inability to distinguish stereoisomers. Examples of 3D QSAR include molecular shape analysis (MSA) [26], distance geometry,and Voronoi techniques [27]. The MSA method utilizes shape descriptors and MLR analysis, whereas the other two approaches apply atomic refractivity as structural descriptor and the solution of mathematical inequalities to obtain the quantitative relationships. These methods have been applied to study structure-activity relationships of many data sets by Hopfinger and Crippen, respectively. Perhaps the most popular example of the 3D QSAR is the com-... 

Can you imagine atoms connected together to form a molecule shaped like a minuscule soccer ball How about connections that result in molecular tubes Remarkably, the element carbon can form these molecular shapes. Perhaps even more remarkably, chemists did not discover this until late in the twentieth century. 

To draw a Lewis stmcture correctly, we must know how the atoms are connected. The guidelines help us do this. The Lewis stmcture does not have to match the actual three-dimensional molecular shape, so we can arrange the framework in any convenient way. 

The Lewis stmcture of a molecule shows how the valence electrons are distributed among the atoms. This gives a useful qualitative picture, but a more thorough understanding of chemistry requires more detailed descriptions of molecular bonding and molecular shapes. In particular, the three-dimensional structure of a molecule, which plays an essential role in determining chemical reactivity, is not shown directly by a Lewis structure. 

Having introduced methane and the tetrahedron, we now begin a systematic coverage of the VSEPR model and molecular shapes. The valence shell electron pair repulsion model assumes that electron-electron repulsion determines the arrangement of valence electrons around each inner atom. This is accomplished by positioning electron pairs as far apart as possible. Figure 9-12 shows the optimal arrangements for two electron pairs (linear),... 

Figure 9-16 shows the molecular shapes of methane, ammonia, and water, all of which have hydrogen ligands bonded to an inner atom. These molecules have different numbers of ligands, but they all have the same steric number. 

Our approach to these molecules illustrates the general strategy for determining the electron group geometry and the molecular shape of each inner atom in a molecule. The process has four steps, beginning with the Lewis structure and ending with the molecular shape. 

The carbon atom in CO2 has two groups of electrons. Recall from our definition of a group that a double bond counts as one group of four electrons. Although each double bond includes four electrons, all four are concentrated between the nuclei. Remember also that the VSEPR model applies to electron groups, not specifically to electron pairs (despite the name of the model). It is the number of ligands and lone pairs, not the number of shared eiectrons, that determines the steric number and hence the molecular shape of an inner atom. 

Use the Lewis structure of CIF3 to determine the steric number of the chlorine atom. Obtain the molecular shape from the orbital geometry after placing lone pairs in appropriate positions. 

Three common molecular shapes are associated with octahedral electron group geomehy. Most often, an inner atom with a steric number of 6 has octahedral molecular shape with no lone pairs. Example uses a compound of xenon, whose chemical behavior is described in the Chemical Milestones Box, to show a second common molecular shape, square planar. 

The square pyramidal geometry of CIF5 completes our inventory of molecular shapes. Figure 9-26 summarizes the characteristics of atoms with steric number 6. 

Dipole moments also depend on molecular shape. Any diatomic molecule with different atoms has a dipole moment. For more complex molecules, we must evaluate dipole moments using both bond polarity and molecular shape. A molecule with polar bonds has no dipole moment if a symmetrical shape causes polar bonds to cancel one another. 

This relatively small catalog of molecular shapes accounts for a remarkable number of molecules. Even complicated molecules such as proteins and other polymers have shapes that can be traced back to these relatively simple templates. The overall shape of a large molecule is a composite of the shapes associated with its inner atoms. The shape around each inner atom is determined by steric numbers and the number of lone pairs. 

C09-0081. Name the molecular shape of an inner atom that has the following characteristics (a) two lone... 

C09-0082. Name the molecular shape of an inner atom that has the following characteristics (a) two lone pairs and steric number of 6 (b) two ligands and three lone pairs (c) one lone pair and five ligands and (d) steric number of 5 and two lone pairs. 

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