Intermolecular Effects

When molecules are in a condensed phase such as a liquid or solid or as a specie intercalated in a DNA double helix structure (discussed in Chapter 3), they can interact with each other through a number of different types of interactions. Examples of these interactions are: (i) weak van der Waals interactions (even occurring among neutral molecules); (ii) intermolecular charge transfer interactions whereby one type of molecule (electron donor) transfers an electron, when in excited state, to another type of molecule (electron acceptor); (iii) electrostatic interactions between charged molecular groups; and (iv) specific chemical association such as hydrogen bonding or even chemical bonding (such as that of various monomeric units to form a polymer). These interactions are discussed in detail in Chapter 3.

These interactions produce a modification of the quantized states of individual molecular units (Prasad, 1997). First, a molecule experiences a static potential field due to all other surrounding molecules, which produces a shift of its energy levels. Next, a dynamic resonance interaction between molecules leads to excitation exchange (energy transfer) of the excitation from one molecule to another. It is like the case of coupled pendulums in which oscillation (excitation) of one pendulum is transferred to another. This excitation interaction is also described by the mixing of their excited energy states. If the molecules are identical, the mixing of their excited energy states, which are degenerate (same value), leads to splitting in a manner similar to the one described by the Hückel theory. For example, mixing of a specific excited energy state of identical molecules A and B produces a splitting, D, leading to two new levels E+ with a plus (symmetric) combination and E_ with a minus

Monomer J-aggregate

Figure 2.20. J-aggregate of a dye.

Monomer J-aggregate

Figure 2.20. J-aggregate of a dye.

(antisymmetric) combination of wave functions of A and B, respectively. The magnitude of the splitting, D, depends on the strength of the interaction between A and B. The new excited energy states are delocalized (spread) over both molecules A and B (just like the delocalization of the p electrons in the case of the Huckel theory). In the case of N identical molecules interacting together, the excited energy states split into N levels, forming a band for a large value of N (like in the case of a conjugated structure with a very long chain length). This description of an energy band formation applies to both the electronic and vibrational energy excitations of molecules. The band is called an exciton band.

Exciton interaction produces a profound effect on the optical properties of fluorescent dyes used for fluorescent tagging in bioimaging and biosensing. Some dyes, when aggregated, form a J-aggregate with new red-shifted exci-tonic states (Kobayashi, 1996). The J-aggregates represent a structure in which dye molecules align in a certain orientation, as shown in Figure 2.20.

Dyes like fluorescein show concentration quenching derived from dimer and higher aggregates formation (Lakowitcz, 1999). As the fluorescence quenching occurs between identical molecules, it is also called self-quenching.

Zhuang et al. (2000) have shown that this type of concentration quenching (self-quenching) can be used to study protein folding at the single-molecule level by attaching multiple dyes to a protein. Folding brings the dyes in close proximity to cause self-quenching, while unfolding moves them apart to reduce self-quenching. Interaction of energy levels between two different molecules produces the shift of their energy levels as well as a unidirectional energy transfer from the higher excited level of one molecule (energy donor) to a lower energy level of another molecule (energy acceptor). This type of electronic energy transfer, called Forster energy transfer, forms the basis for fluorescence resonance energy transfer (FRET) bioimaging discussed in Chapter 7. The Forster energy transfer is discussed in Chapter 4.

Another type of interaction which occurs between an electron-rich molecule (electron donor) and an electron-deficient molecule (electron acceptor) through an excited-state charge transfer produces new quantized electronic levels called charge-transfer states. The charge-transfer states are new excited states in which an electron is partially (or largely) transferred from the electron donor to the electron acceptor. The absorption from the ground state to the charge-transfer state often makes otherwise colorless electron-donating and electron-accepting molecules acquire colors, due to the absorption being in the visible spectral range.

Another major manifestation of placing a molecule in an ensemble of molecules is that its rotational and translational motions are hindered (spatially restricted). As a result, these motions become to-and-fro vibrations, called phonons or lattice vibrations. The lattice vibrations or phonons are of frequencies in the range of 0-200cm-1. The phonons are very sensitive to intermolecular arrangements of the molecules in the solid form, so they can be used as a fingerprint of a given lattice structure. The phonons, as observed by Raman spectroscopy (discussed in Chapter 4), have been shown to be very useful for characterizing different crystalline forms, called polymorphic forms, of a drug (Bellows et al., 1977; Resetarits et al., 1979; Bolton and Prasad, 1981). Such information is very useful for drug formulation since it has been shown that the bioavailability of a drug (dissolution rate and subsequent action) depends on its polymorphic form (Haleblian and McCrone, 1969; Haleblian, 1975).

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