Molecular Configurations

Type of physical science: Chemistry

Field of study: Chemistry of molecules: nature of chemical bonds

The physical and chemical characteristics of a material or compound are directly related to the configuration of the component molecules. In order to understand these properties, one must study the geometric shape of the molecular units making up the material, the intermolecular chemical forces, and the interactions between neighboring molecules.

Overview

The geometric arrangement of component atoms and the manner in which these atoms are bonded together define the configuration of the molecule. The general shape of the molecule, which may be described as linear, planar, or spherical, can be directly related to the molecular configuration. Isomers may exhibit distinctly different shapes resulting from differences in bonding sequences. From a practical perspective, the major significance of understanding molecular configurations is that the physical and chemical properties of a compound are directly correlated with this phenomenon. Density and viscosity of liquid compounds are reflective of molecular configurations and the associated interactions. Large molecules with branching side chains tend to form viscous liquids and solids. Small, roughly spherical molecules tend to interact less; thus, they reside in the gas phase.

The overall geometric shape of the molecule is one aspect of the configuration. Atoms bonded together in a linear fashion form chainlike structures. These compounds can exhibit straight, linear geometries or form helices of coiled, intertwining structures. Additional atoms can be added to form branches from the main chain. If the ends of these chains are connected, ring structures are generated. For these cyclic systems, the geometric shape may be planar, for a rigid ring system, or nonplanar "zigzag," for a larger molecule. If the atoms that are branched from rings bond together, complex polyhedral molecules are formed. Depending on the flexibility of the system, these molecules can exhibit spherical, oblate, or elliptical shapes. For large systems, these molecules can resemble molecular-scale cages formed by interconnected rings of atoms.

The molecular configuration is strongly influenced by the types of chemical bond present in the compound. The types of atom present in the molecule limit the diversity of configurations. The coordination number of an atom must be consistent with the number of valence electrons available for bond formation. In a molecular system, an atom cannot be bonded to more adjoining atoms than can be accommodated by its valence electrons. For example, with the exception of some hydrides, hydrogen atoms are bonded to a single atom only. This is consistent with the hydrogen atom having a single valence electron. For atoms with p-type valence electrons, such as the carbon atom, the situation is more interesting. Depending on the type of chemical bond formed, a carbon can be bonded to one, two, three, or four neighbors, forming single, double, or triple bonds. This can be rationalized in terms of atomic orbitals and their interactions to form chemical bonds. If each of the four carbon valence electrons contribute equally to the chemical bonding, four roughly equivalent bonds are formed. This is observed in methane (CH₄). This behavior is explained in terms of the hybridization, or mixing, of atomic orbitals. In this case, the single-carbon two s-orbital is hybridized, or mixed, with the three-carbon two pvalence orbitals to form four new bonding orbitals. These orbitals are denoted as sp³ hybrids and form a tetrahedral arrangement around the carbon. If the carbon is bonded to less than four neighboring atoms, combinations of one s-orbital and two p-orbitals, sp² hybrids, and orbitals of one each of the s- and p-orbitals, sp hybrids, can be generated. In each of these cases, the remaining valence electrons go into forming multiple bonds arising from the interactions of the remaining carbon porbitals. Hybridization implies certain geometric arrangements, further restricting the possible configurations for a molecule. For example, a carbon atom with sp² hybrid orbitals must form a planar molecule, and one with sp hybrids must bond in a linear fashion. In all of these cases, the total valence electrons contributed by the two atoms forming the bond must be consistent with the number and strength of the bonding interactions.

The diversity of molecular configurations is governed primarily by the number of atoms in the molecule. As the size of the system increases, so does the range of possible geometries and configurations. For a diatomic molecule, A-B, the configuration is very simple; the system must be linear. With the addition of the third atom to form a compound A-B-C, the choices of bonding character and geometry increase. If A is bonded to B and B is also bonded to C, the system can be either linear or bent. If an additional bond is added between C and A, a planar ring structure can be obtained. This progression of molecular size and complexity of configuration continues as more atoms are added to the system. A four-atom molecular configuration could be linear, bent, T-shaped, Y-shaped, polyhedral (for example, a four-atom tetrahedral cluster), or a four-membered ring (planar or butterfly-shaped). Each of these isomers would correspond to distinct bonding patterns and exhibit different chemical and structural properties. Some isomers may not be of practical relevance if the valence electrons in the system are inconsistent with the proposed bonding arrangement. As the number of atoms becomes larger, the chainlike configurations become more common. In these cases, the diversity in configuration arises from the endless variety of possible side chains, as well as the structural features associated with the chains folding, intertwining, and forming ordered helical structures.

The overall symmetry of the molecule will also affect the number and variety of molecular configurations. The presence of chemically and symmetrically equivalent atoms simplifies the enumeration of isomers. For example, in a planar ring system, if all the ring atoms are of the same symmetry, the ring geometry will correspond to a regular polygon. In addition to atoms, bonds and molecular subunits can be analyzed in terms of symmetry relationships. In methane (CH4), all the C-H bonds are equivalent; therefore, only certain classes of geometry need be considered, in this case only regular tetrahedral, pyramidal, or square planar. In polymers, a large molecule is formed by the repeated addition of identical submolecules to the ends of a starting molecule. Therefore, the analysis of this complex system can be simplified by focusing on the characteristics of the repeating unit.

The presence of long-range and nonbonded interactions may strongly influence the configurations of complex molecules. Nearest-neighbor bonding can explain most aspects of molecular configuration, but for larger systems such as proteins, polymers, and complex organic ring systems, these more subtle effects determine the molecular geometry. The folding of proteins is strongly controlled by the relatively weak hydrogen bonding interactions between atoms in the molecule. For example, these longer-range interactions may favor certain helical forms or other structures corresponding to decreased repulsive interactions. The conformation of many organic molecules is strongly influenced by steric interaction between large groups of atoms attached to a ring or chain. As would be expected, the stable isomers tend to minimize the crowding of large, bulky atoms and substituted groups in one spatial region of the system.

Molecules subjected to normal laboratory conditions are dynamic systems, not static objects. Their internal vibrational and rotational motions can be directly related to their configuration. The total number of degrees of freedom of a molecule must be equal to three times the number of atoms in the molecule. In other words, the total of the types of possible translation, rotational, and vibrational motion must be consistent with the number of atoms in the system. At this point, no account is given to the bonding or molecular geometry. Three of these motions can be attributed to the translation of the center of mass of the molecule. This center of mass will depend on the molecular configuration. For a nonlinear molecule, three additional degrees of freedom are associated with rotational motion around the center of mass. The remaining three to six times the number of degrees of freedom are then used to describe the vibrational motion of the atoms in the system.

Characterizing the vibrational motion gives direct information about the configuration.

Since vibrations are attributed to the compression/expansion of a bond or bond angle, two isomers will normally exhibit different types of vibrations. For example, a carbon-carbon single bond has a distinct vibrational frequency, compared to either a double- or triple-bonded carbon system. This permits the use of vibrational spectroscopy for the identification of organic compounds. Different isomers may also exhibit variations in the rotational motion. For larger, complex molecules, these degrees of freedom may include rotations of groups of atoms about bonds, dihedral angular motions, and long-range twisting modes.

Applications

For many chemical compounds, the property of a material that makes it useful to society is based on the molecular configuration. In this context, the chemical reactivity is considered a separate issue from the structural properties. The importance of molecular configurations in determining material properties can be seen in two familiar examples.

Polymers are one of the more common and important types of material one encounters in daily life. Materials often taken for granted, such as rubber, synthetic fibers, and plastic, are polymeric materials. Polymers are compounds with large molecular weights synthesized by the addition of molecular fragments to the ends of an existing molecule. The molecule added to form the polymer can be different or identical to the molecule to which it is added. In most cases, it is desirable to produce a final product with an ordered arrangement of these subunits.

By design, most commercial polymers are chemically inert materials. Physical properties range from transparent to opaque, spongy to very hard, and dense to air-filled foam.

Therefore, the choice of materials for a particular application will depend on the technological problem. For any polymeric compound, the characteristics of the final product are related to molecular configuration. From the technological perspective, this is a very advantageous situation. Desirable polymeric features, such as high density or stiffness, can be designed into the system by suitably controlling the configurations of the molecules making up the material.

The elasticity of polymers can be attributed to the general shapes of polymer molecules and to the way neighboring molecules interact. A material will be elastic if the component molecules are very flexible and are able to move smoothly relative to nearby molecules. If either of these conditions is absent, it is hard to produce an elastic polymer.

The chemical aspect of polymer properties is best reflected in the thermal stability, or melting point. The stability of polymers at elevated temperatures is dependent on several factors.

First, the chemical inertness of the component molecule must be analyzed. For practical applications, most common polymer building blocks, such as ethylene, are stable. The thermal breakdown can usually be attributed to changes reflective of molecular configuration.

Cross-linking between adjacent molecules enhances the structural stability by adding more bonding interactions to the system. These interpolymer bonds have ramifications on the density of the resulting material. A low-density polymer would have relatively large spaces between neighboring molecules. This could be accomplished by adding side chains to the main polymer backbone. Taken to an extreme, these side chains could actually connect adjacent polymers, resulting in sheets and networks of connected polymer molecules. The low-density materials are often produced by bubbling air or gas through a polymer reaction mixture. With the gas present, the polymer reaction is initiated, forming an open network of linked polymer molecules.

Another very important class of chemical compound is hydrocarbons. These provide fuels for automobiles and airplanes, lubricants for engines, and source material for the synthesis of other chemical compounds such as polymers. During the petroleum refining process, the crude oil mixture is fractionated into the various hydrocarbon compounds by gradually raising the temperature of the mixture. The low-boiling liquids and gases are extracted first, followed by the oils and solids of higher molecular weight. Even though all of these compounds consist primarily of carbon and hydrogen, a diverse range of structures and physicochemical properties can occur.

Hydrocarbons with low molecular weights (compounds containing one to three carbons) exist as gases at normal pressure.

Middle-weight compounds form liquids. Both classes provide valuable sources of fuel.

Heavier hydrocarbons are used for lubricating oils. Many compounds with higher molecular weights may also form solids, such as paraffin and asphalt.

Methane, the simplest hydrocarbon, consists of four hydrogen atoms bonded to a single carbon atom (CH₄). All the bonds are symmetrically equivalent and form a tetrahedral arrangement. Combining two methane molecules with a carbon-carbon bond yields ethane (C₂H₆), adding a third generates propane (C₃H₈), and so on. As the size of the molecule increases, the boiling point increases. Simple linear-chain hydrocarbons involving five to eight carbons form the mixture known as gasoline. The addition of more carbons, via branched chains or rings, raises the boiling point significantly. This results in compounds that are stable even under the extreme temperature and pressure conditions of an internal combustion engine. Since these molecules have higher molecular weights (more atoms), they can exist in a large variety of configurations. The chemical stability is enhanced by the presence of strong carbon-carbon multiple bonds, as well as interconnected rings. The large molecular size, combined with enhanced interactions between neighboring molecules, tends to favor the formation of liquids and solids.

Context

The interactions of electrons and nuclei that give rise to stable molecules are also responsible for determining the configuration of a molecule. Theoretical chemical methods, based on classical physics and quantum mechanics, provide valuable models of these intermolecular forces. Absorption spectroscopy is an experimental technique for directly probing molecular properties, geometry, and bonding character. This method gives direct insight into the often subtle aspects of the chemical interactions responsible for the formation of isomers.

The configuration of a molecule is a direct consequence of the chemical bonding in the compound. Quantum mechanics provides the tools to explain the structure and reactivity of chemical systems in terms of fundamental interactions of electrons and nuclei. For molecules, the energies associated with different configurations can be determined using molecular orbital theory. In this approach, the bonding electrons in molecules are described using linear combinations of atomic orbitals. Chemical bonds are then described by focusing on the interactions of atomic orbitals located on adjacent atoms. Certain types of interactions stabilize the system, forming chemical bonds, while other interactions will actually decrease molecular stability. Using this approach, changes in coordination number, bonding character, and geometry can be investigated in rigorous detail. In principle, even subtle features of the structure, such as long-range hydrogen bonding interactions, can be analyzed. Unfortunately, because of practical limitations, these methods are most useful for relatively small molecules.

For larger systems, molecular mechanics, which is based on classical physics, provides a tool for analyzing and modeling molecular configurations. In this approach, the optimized molecular configuration is defined as the geometry that generates the least strain energy. Several factors contribute to the total molecular strain energy. First, the energy associated with the compression or expansion of specific bonds, relative to equilibrium values, is determined. Every bond in the molecule is described with a characteristic strain energy constant. Second, angular terms are added to account for the strain arising from bending angles, including dihedrals, from equilibrium values. In addition, long-range nonbonding interactions and terms accounting for coupled stretching-bending can be included. As long as the individual strain contributions are accurately modeled, molecular mechanics provides a very useful tool for predicting molecular configurations.

Experimental techniques also contribute to an understanding of molecular configuration. Spectroscopy provides information concerning the geometry and bonding character of a molecule. In most cases, the way in which a molecule absorbs radiation is interpreted in terms of specific properties of the molecular system. Quantum mechanics shows that only certain energy levels are possible for molecular systems. This holds for rotational, vibrational, and electronic energy levels. Spectroscopic methods measure the spacing of these energy levels. By properly choosing the wavelength of the radiation, one can study each of these types of molecular motion. Light in the ultraviolet/visible range will excite electrons from lower to higher electronic states. This information can then be compared to the energy levels predicted using quantum mechanics. Infrared radiation is of the appropriate energy to excite molecular vibrations. By scanning over a range of wavelengths, each vibrational absorption can be assigned to a particular bond-stretching or angle-bending mode in the molecule. This provides a means to fingerprint a complicated molecule in terms of component parts. Moving down the energy spectrum, microwave radiation is used to excite rotational levels in a compound. The spacings between the lines in this spectrum give information that can be used to calculate the geometry of a molecule.

The value of each of these spectroscopic tools is greatly enhanced if each is used in conjunction with the theoretical methods. Conversely, the usefulness of theoretical approaches is greatly expanded if they are interpreted in the light of observed spectroscopic data. By using both chemical theory and experimental spectroscopy, one can obtain a more complete representation of the configurations of a molecular system and the resulting physical and chemical properties.

Principal terms

ATOMIC ORBITALS: the electrons associated with an atom found to exist in discrete orbitals, or states, having quantized energies; the electron charge density for the lowest-energy, "s-type" orbitals is spherical; the higher-energy, "p-type" orbitals are two-lobed (dumbbell-shaped); and the "d-type" orbitals have four lobes (cloverleaf)

COORDINATION NUMBER: the number of adjacent atoms directly associated with the atom of interest; in molecules, this is equal to the number of bonded neighbors and must be consistent with the number of valence electrons

DEGREES OF FREEDOM: the number of modes or types of possible motion for a molecule, normally partitioned into translational, vibrational, and rotational contributions; reflective of the type of bonds holding the molecule together

HELIX: a spiral arrangement exhibited by long chain molecules; the direction of the spiral (clockwise or counterclockwise) and the pattern describing the repeating units define the configuration

ISOMERS: chemical compounds with the same chemical formula (identical atomic composition), but with atoms bonded together in different ways; often exhibit distinct chemical and physical properties

TETRAHEDRAL: a geometry commonly adopted by five-atom molecules, or portions of molecules, with the general formula AX sub 4, in which all A-X bonds are equivalent and each of the X-A-X angles equals 109.5 degrees

VALENCE ELECTRONS: the relatively loosely held electrons associated with an atom that participate in the chemical bonding process; two valence electrons form each bond in a molecule

Bibliography

Barrow, Gordon M. THE STRUCTURE OF MOLECULES: AN INTRODUCTION TO MOLECULAR SPECTROSCOPY. Menlo Park, Calif.: W. A. Benjamin, 1963. Barrow provides a clear survey of the relationship between molecular motion and configuration. He covers the fundamentals of molecular spectroscopy, vibrational, rotational, and electronic, and how each technique elucidates structural properties of a compound.

Gray, Harry. CHEMICAL BONDS: AN INTRODUCTION TO ATOMIC AND MOLECULAR STRUCTURE. Menlo Park, Calif.: W. A. Benjamin, 1973.

Gray, Harry. ELECTRONS AND CHEMICAL BONDING. Menlo Park, Calif.: W. A. Benjamin, 1964. Starting from the concepts of atomic electronic structure theory, these books proceed to develop the relationship between molecular geometry and chemical bonding. The concepts of valency, hybridization, and multiple bonds are illustrated for simple organic molecules. In addition, the diverse range of molecular geometries are also surveyed in the context of chemical bonding concepts.

Mark, Herman F. GIANT MOLECULES. New York: Time, 1966. This book surveys synthetic polymers and the applications of these materials to everyday usage. Conformational features of Teflon, synthetic fibers, rubber, and other man-made "wonder" materials are discussed in a historical context. The relationships between polymer structure and the resulting chemical and physical properties are summarized for a wide variety of compounds. In addition, the book discusses the relationship between hydrocarbons and the synthesis of a variety of polymeric materials.

Pauling, Linus, and Roger Hayward. THE ARCHITECTURE OF MOLECULES. San Francisco: W. H. Freeman, 1964. This book provides a pictorial survey of many of the common molecular geometries and configurations. For each type of crystal or molecule, a drawing is used to illustrate the system. Configurational features unique to each structure are pictured and clearly discussed. A broad range of systems are covered, from simple molecules to crystalline structures and biopolymers.

Carbon and Carbon Group Compounds

Quantum Mechanics of Chemical Bonding

Isomeric Forms of Molecules

Calculations of Molecular Structure

Quantum Mechanics of Molecules