Visualization of molecular properties

Knowledge of the spatial dimensions of a molecule is insufficient to imderstand the details of complex molecular interactions. In fact, molecular properties such as electrostatic potential, hydrophilic/lipophilic properties, and hydrogen bonding ability should be taken into account. These properties can be classified as scalar isosurfaces), vector field, and volumetric properties. 

---

In another definition, the term molecular surface has been introduced by Richards describing a molecular envelope accessible by a solvent molecule. These surfaces are used successfully in many chemical investigations, e.g., docking algorithms, free-energy surface density approaches, and visualization of molecular properties. ... 

The representation of molecular properties on molecular surfaces is only possible with values based on scalar fields. If vector fields, such as the electric fields of molecules, or potential directions of hydrogen bridge bonding, need to be visualized, other methods of representation must be applied. Generally, directed properties are displayed by spatially oriented cones or by field lines. 

The visualization of volumetric properties is more important in other scientific disciplines (e.g., computer tomography in medicine, or convection streams in geology). However, there are also some applications in chemistry (Figure 2-125d), among which only the distribution of water density in molecular dynamics simulations will be mentioned here. Computer visualization of this property is usually realized with two or three dimensional textures [203]. 

Since e > eo, we seek to explain the smaller field in the presence of the dielectric in terms of molecular properties and the way in which they are affected by the electric field. An easy way to visualize the effect is to picture an opposing surface charge-indicated as in Fig. 10.4b—accumulating on the dielectric. This partially offsets the charge on the capacitor plates to a net charge density a - so that Eq becomes E and is given by... 

Very striking results on the interactions of molecules with a catalyst have been recently reported in zeolite catalysis because of the well ordered structure of these materials it is worth mentioning the subjects of zeolite design [10] and of acidic properties of metallosilicates [11]. In other areas where polycrystallinic or even amorphous materials arc applied, highly interesting results are now numerously emerging (such as hydrocarbon oxidation on vanadium-based catalysts [12] location of transition metal cations on Si(100) [13] CO molecules on MgO surfaces [14] CH4 and O2 interaction with sodium- and zinc-doped CaO surfaces [15] CO and NO on heavy metal surfaces [16]). An illustration of the computerized visualization of molecular dynamics of Pd clusters on MgO(lOO) and on a three-dimensional trajectory of Ar in Na mordenitc, is the recent publication of Miura et al. [17]. 

The molecular surface concept is not only useful for a representation of the bulkiness and the shape of molecules. These surfaces can also be used as screens for the visualization of many properties by means of color coding techniques. Color coding is a popular means of displaying scalar information on a surface. " " Every three-dimensional scalar or vector field that may be generated on the basis of the position of atomic or molecular fragments can be visualized by color coding on a given surface. 

In the second part (Sections 6.4-6.7) we will consider what the vibrations belonging to a given irreducible representation look like . This involves the construction of linear combinations of the basis of atomic movements that are consistent with the characters of the irreducible representation. These combinations are known as symmetry adapted linear combinations (SALCs). SALCs are a general way to visualize the molecular properties that correspond to the objects with the irreducible symmetries identified by the reduction formula. The method we shall use to obtain these SALCs is the projection operator, which is introduced in Section 6.6 and will also be employed in Chapter 7 to find molecular orbitals. 

The shape, electronic properties, and chemical stability of the bio-macromolecule and ligand are important factors because they determine how well the lock is occupied by the key. Computational chemistry provides powerful tools to help the chemist to simulate and visualize these molecular properties, as well as to refine raw experimental data on receptor structures. 

Besides molecular orbitals, other molecular properties, such as electrostatic potentials or spin density, can be represented by isovalue surfaces. Normally, these scalar properties are mapped onto different surfaces see above). This type of high-dimensional visualization permits fast and easy identification of the relevant molecular regions. 

Optical Properties. When light falls on an object, it is either partially absorbed, reflected, or transmitted. The behavior of the object as it relates to each of these three possibiUties determines visual appearance. Optical properties of fibers give useful information about the fiber stmcture refractive indexes correlate well with fiber crystalline and molecular orientation and birefringence gives a measure of the degree of anisotropy of the fiber. 

We contend therefore that introduction of molecular modeling very early into the currieulum need not complicate or eonfuse the learning of organie chemistry, but rather assist the student in visualizing the structures of organic molecules and in learning the intimate connections between molecular structure and molecular properties. 

Molecular modeling itself can be simply described as the computer-assisted calculation, modulation, and visualization of realistic 3D-molecular structures and their physical-chemical properties using force fields/ molecular mechanics. 

The total molecular energy is invariant to all transformations involving basis orbitals, just as any physical event is invariant under any transformation of coordinates. But just as the proper choice of coordinates helps in visualizing physical events, so the choice of the proper orbital basis is helpful in visualizing molecular properties. 

Molecular modeling seeks to answer questions about molecular properties— stabilities, reactivities, electronic properties—as they are related to molecular structure. The visualization and analysis of such structures, as well as their molecular properties and molecular interactions, are based on some theoretical means for predicting the structures and properties of molecules and complexes. If an algorithm can be developed to calculate a structure with a given stoichiometry and connectivity, one can then attempt to compute properties based on calculated molecular structure and vice versa. 

---