Interaction between Molecules

The interaction between the molecules in coffee that taste bitter and the taste receptors on the tongue is caused by intermolecular forces—attractive forces that exist between molecules. Living organisms depend on intermolecular forces not only for taste but also for many other physiological processes. For example, in Chapter 19, we will see how intermolecular forces help determine the shapes of protein molecules—the workhorse molecules in living organisms. Later in this chapter—in the Chemistry and Health box in Section 12.6—we learn how intermolecular forces are central to DNA, the inheritable molecules that serve as blueprints for life. 

The interactions between bitter molecules in coffee and molecular receptors on the tongue are highly specific. However, less specific intermolecular forces exisf between all molecules and atoms. These intermolecular forces are responsible for the very existence of liquids and solids. The state of a sample of matter— solid, liquid, or gas—depends on the magnitude of intermolecular forces relative to the amoimt of thermal energy in the sample. Recall from Section 3.10 that the molecules and atoms that compose matter are in constant random motion that increases witir increasing temperature. The energy associated with this motion is 

One of the most useful applications of the symmetry and perturbation theories is to interactions between molecules. 

7 For further discussion of hyperconjugation, see (a) M. J. S. Dewar, Hyperconjugation, Ronald Press, New York, 1962 (b) D. Holtz, Prog. Phys. Org. Chem., 8, 1 (1971). 

Qualitative arguments based on the HOMO-LUMO theory are applicable to a variety of chemical processes.8 Consider as an example Reaction 10.10. Will this 

Klopman has applied HOMO-LUMO arguments to hard-soft Lewis acid—base theory.10 Although his treatment is a quantitative one, we shall describe only its 

In Klopman s quantitative calculations, the presence of other orbitals close in energy to the frontier orbitals is taken into account in the determination of the reactivity, as is the change in solvation energy on complex formation. On these theoretical grounds, Klopman has been able to classify Lewis acids and bases into hard, soft, and borderline categories his results closely parallel Pearson s assignments (Section 3.5) made from consideration of chemical properties. 

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The surface free energy can be regarded as the work of bringing a molecule from the interior of a liquid to the surface, and that this work arises from the fact that, although a molecule experiences no net forces while in the interior of the bulk phase, these forces become unbalanced as it moves toward the surface. As discussed in connection with Eq. Ill-IS and also in the next sections, a knowledge of the potential function for the interaction between molecules allows a calculation of the total surface energy if this can be written as a function of temperature, the surface free energy is also calculable. 

Perturbation theory yields a siim-over-states fomnila for each of the dispersion coefficients. For example, the isotropic coefficient for the interaction between molecules A and B is given by... 

The approach described in section Al.5.5.3 is best suited for accurate representations of the PES for interactions between small molecules. Interactions between large molecules are usually handled with an atom-atom or site-site approach. For example, an atom-atom, exp-6 potential for the interaction between molecules A and B can be written as... 

Computer simulations act as a bridge between microscopic length and time scales and tlie macroscopic world of the laboratory (see figure B3.3.1. We provide a guess at the interactions between molecules, and obtain exact predictions of bulk properties. The predictions are exact in the sense that they can be made as accurate as we like, subject to the limitations imposed by our computer budget. At the same time, the hidden detail behind bulk measurements can be revealed. Examples are the link between the diffiision coefficient and... 

Molecular dynamics consists of the brute-force solution of Newton s equations of motion. It is necessary to encode in the program the potential energy and force law of interaction between molecules the equations of motion are solved numerically, by finite difference techniques. The system evolution corresponds closely to what happens in real life and allows us to calculate dynamical properties, as well as thennodynamic and structural fiinctions. For a range of molecular models, packaged routines are available, either connnercially or tlirough the academic conmuinity. 

Non-covalent interactions between molecules often occur at separations where the van der Waals radii of the atoms are just touching and so it is often most useful to examine the electrostatic potential in this region. For this reason, the electrostatic potential is often calculated at the molecular surface (defined in Section 1.5) or the equivalent isodensity surface as shown in Figure 2.18 (colour plate section). Such pictorial representations... 

For examining the interactions between molecules, use electrostatic charges. 

Completely ah initio predictions can be more accurate than any experimental result currently available. This is only true of properties that depend on the behavior of isolated molecules. Colligative properties, which are due to the interaction between molecules, can be computed more reliably with methods based on thermodynamics, statistical mechanics, structure-activity relationships, or completely empirical group additivity methods. 

Nearly all liquid simulations have been done using molecular mechanics force fields to describe the interactions between molecules. A few rare simulations have been completed with orbital-based methods. It is expected that it will still be a long time before orbital-based simulations represent a majority of the studies done due to the incredibly large amount of computational resources necessary for these methods. 

Our major objectives m this chapter are to develop a feeling for molecules as three dimensional objects and to become familiar with stereochemical principles terms and notation A full understanding of organic and biological chemistry requires an awareness of the spatial requirements for interactions between molecules this chapter provides the basis for that understanding... 

The coefficient Bij characterizes a bimolecular interaction between molecules i and J, and therefore Bij = Bji. Two lands of second virial coefficient arise Bn and By, wherein the subscripts are the same (i =j) and Bij, wherein they are different (i j). The first is a virial coefficient for a pure species the second is a mixture property, called a cross coefficient. Similarly for the third virial coefficients Cm, Cjjj, and are for the pure species and Qy = Cyi = Cjn, and so on, are cross coefficients. 

This dispersion interaction must be added to the dipole-dipole interactions between molecules, such as HCl, NH3 and H2O which have a permanent dipole, fi. The magnitude of die dipole moment depends on tire differences in electronegativity of the atoms in the molecule. Here again, the energy of interaction varies as (orientation effect). 

A simple model for interactions between particles in an associating bulk fluid consists of a particle-particle potential and the interactions between sites belonging to different molecules. Supposing that each molecule has M sites, the potential of interaction between molecules 1 and 2 is [14]... 

Approximating the intermoleculai interactions to only include two-body effects, e.g. electrostatic forces are only calculated between pairs of fixed atomic chai ges in force field techniques. Or the discrete interactions between molecules may be treated only in an average fashion, by using Langevin dynamics instead of molecular dynamics. 

When thinking about chemical reactivity, chemists usually focus their attention on bonds, the covalent interactions between atoms within individual molecules. Also important, hotvever, particularly in large biomolecules like proteins and nucleic acids, are a variety of interactions between molecules that strongly affect molecular properties. Collectively called either intermolecular forces, van der Waals forces, or noncovalent interactions, they are of several different types dipole-dipole forces, dispersion forces, and hydrogen bonds. 

Dispersion force (Section 2.13) A noncovalent interaction between molecules that arises because of constantly changing electron distributions within the molecules. 

Noncovalcnt interaction (Section 2.13) An interaction between molecules, commonly called intermolecular forces or van der VVaals forces. Hydrogen bonds, dipole-dipole forces, and dispersion forces are examples. 

For most exopolysaccharides their shape is determined by the angle of bonds which governs the relative orientations of adjacent sugar residues in the chain. However, die range of relative orientations of adjacent sugar molecules is limited by steric interactions between molecules along the chain. 

The intermolecular interactions stabilise the helices and greatly influence the properties of exopolysaccharides in solution, ie solubility, viscosity and gel-formation. A strong interaction or good-fit between molecules will lead to insolubility, whereas poor interaction will lead to solubility of exopolysaccharides. The interactions between molecules is influenced by the presence of side-chains. For example, cellulose is insoluble but introduction of a three monosaccharide side-chain into the cellulose chain gives the soluble xanthan. Small changes in the structure of the side-chains can alter the molecular interactions and thus properties of the exopolysaccharide. 

Johannes van der Waals was a Dutch scientist who studied the interactions between molecules see Chapter 4. 

The London interaction is universal in the sense that it applies to all molecules regardless of their chemical identity. Similarly, the dipole-dipole interaction depends only on the polarity of the molecule, regardless of its chemical identity. However, there is another very strong interaction between molecules that is specific to molecules with certain types of atoms. 

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