Shape-Dependent Molecular Properties

In addition to the geometric, steric effects which flexibility directly modifles, all intramolecular electronic properties of a flexible molecule are also coupled to molecular structure. In a real material, such properties as molecular dipole. 

In some molecules the molecular dipole is simply dominated by a single polar bond. In sufficiently complex molecules there may be several polar bonds of differing strength. In this case the molecular dipole is determined by their relative orientation. Ab initio studies of 2-2 -difluoro biphenyl have revealed a strong shape dependence of the molecular dipole as a function of inter-ring angle. This is illustrated in Fig. 12. 

---

The STO-3G wavefunction does not have a cusp at the nucleus. Very few molecular properties depend on the exact shape of the wavefunction at the nucleus ... 

A molecule is a three-dimensional array of atoms. In fact, many of a molecule s properties, such as its odor and chemical reactivity, depend on its three-dimensional shape. Although molecular and structural formulas describe the composition of a molecule, they do not represent the molecule s shape. To provide information about shapes, chemists frequently use ball-and-stick models or space-filling models. 

The dynamic behavior of fluid interfaces is usually described in terms of surface rheology. Monolayer-covered interfaces may display dramatically different rheological behavior from that of the clean liquid interface. These time-dependent properties vary with the extent of intermolecular association within the monolayer at a given thermodynamic state, which in turn may be related directly to molecular size, shape, and charge (Manheimer and Schechter, 1970). Two of these time-dependent rheological properties are discussed here surface shear viscosity and dynamic surface tension. 

Random-coil sequences left in a predominantly helical chain can be a cause of flexibility of the molecular rod unless they are too short, and will lead to deviations of the shape-dependent properties of the molecule from those expected for rigid rod. Too short a random-coil sequence may not act as a flexible joint partly because of hindered rotations of the single bonds contained... 

D-QSAR. Since compounds are active in three dimensions and their shape and surface properties are major determinants of their activity, the attractiveness of 3D-QSAR methods is intuitively clear. Here conformations of active molecules must be generated and their features captured by use of conformation-dependent descriptors. Despite its conceptual attractiveness, 3D-QSAR faces two major challenges. First, since bioactive conformations are in many cases not known from experiment, they must be predicted. This is often done by systematic conformational analysis and identification of preferred low energy conformations, which presents one of the major uncertainties in 3D-QSAR analysis. In fact, to date there is no computational method available to reliably and routinely predict bioactive molecular conformations. Thus, conformational analysis often only generates a crude approximation of active conformations. In order to at least partly compensate for these difficulties, information from active sites in target proteins is taken into account, if available (receptor-dependent QSAR). Second, once conformations are modeled, they must be correctly aligned in three dimensions, which is another major source of errors in the system set-up for 3D-QSAR studies. 

This competition between weak hydrogen bonding and polarization of the bromine depends sensitively on molecular properties. For example, consider the case of SCO-HX complexes, for which both SCO-HF and SCO-HC1 have been found to be linear as shown that is, the HX is hydrogen-bonded to the oxygen (Altman et al. 1982 Baiocchi et al. 1981 Fraser et al. 1989 Legon and Willoughby 1985 Shea et al. 1983). These are analogous to C02-HF and C02-HC1. However, it has been discovered recently that SCO-HBr is also linear as shown (Hu and Sharpe 1994 Walker et al. submitted), in contrast to inertially T-shaped C02-HBr. This qualitative structural difference underscores both the subtle competitions that occur in such systems and the need for experimental structural determinations. 

These systems are imperfect models for molecular recognition, since both the potential functions and energy distributions that describe the interactions in MESA are different from those at the molecular level. Moreover, the encounter frequencies between objects in MESA (10 3—10-2 s-1) are much smaller than those between molecules (102-103 s, for micromolar concentrations). Despite these differences, our model manages to exhibit the salient characteristics of molecular recognition assembly depends on the shapes and interfacial properties of the faces that recognize one another. 

The EVA descriptors are among - 3D-descriptors, independent of any molecular alignment, giving information about molecular size, shape and electronic properties. Moreover, the EVA descriptors show only a moderate dependence on conformations. 

Symmetry is an important but often elusive molecular property when numerical values must be assigned. However, symmetry plays an important role in the quantum mechanical interpretation of atomic and molecular states, NMR spectra and several physico-chemical properties. Symmetry is closely related to those molecular properties which also depend on entropy contributions, such as, for example, melting point, vapour pressure, surface tension, and - dipole moment. Moreover, the nature of overall molecular shape depends on molecular symmetry. 

We will first discuss the basic ideas and application of these two theories. Then we will learn how an important molecular property, polarity, depends on molecular shape. Most of this chapter will then be devoted to studying how these ideas are applied to various types of polyatomic molecules and ions. 

Time-domain spectroscopies entail a major shift in emphasis from traditional spectroscopies, since the experimenter can control, in principle, the duration, shape, and sequence of pulses. One may say that traditional, CW spectroscopy, is passive—the experimenter attempts to study static properties of a particular molecule. Coherent pulse experiments are active in that, given a set of molecular properties (which may in fact be known from various spectroscopies), one tries to arrange for a desired chemical product, or to design a pulse sequence that will probe new molecular properties. The time-dependent quantum mechanics-wavepacket dynamics approach developed here is a natural framework for formulating and interpreting new multiple pulse experiments. Femtosecond experiments yield to a particularly simple interpretation within our approach. 

---