Structural properties of molecules

The calculation of the electro-optical parameters describing Raman intensities is not yet very advanced, because of the paucity of data. Nevertheless, some success was achieved in calculations of the intensity of infrared absorption. The results on trans and gauche bond-rotation in ethylene glycol146 could be taken as a model for carbohydrates. Indeed, similar electro-optical parameters (/aCH, /aOH, /aCC, and /aCO) were calculated. This leads to the expectation that calculations of the intensity of the vibrational spectra of carbohydrates may be accomplished in the near future. In addition, the delicate problem of accounting for molecular interactions in calculating infrared intensities could be approached as it was for v(CCC) and i CO) vibrations in acetone.149 This will allow interpretation of weak, as well as strong, i.r. bands, in order to determine the structural properties of molecules. 

The study of molecular interactions in liquid mixtures is of considerable importance in the elucidation of the structural properties of molecules. Interactions between molecules influence the structural arrangement and shape of molecules. Dielectric relaxation of polar molecules in non-polar solvents using microwave absorption has been widely employed to study molecular structures and molecular interactions in liquid mixtures [81]. Ever since Lagemann and Dunbar developed a US velocity approach for the qualitative determination of the degree of association in liquids [82], a number of scientists have used ultrasonic waves of low amplitude to investigate the nature of molecular interactions and the physico-chemical behaviour of pure liquids and binary, ternary and quaternary liquid mixtures, and found complex formation to occur if the observed values of excess parameters (e.g. excess adiabatic compressibility, intermolecular free length or volume) are negative. These parameters can be calculated from those for ultrasonic velocity (c) and density (p). Thus,... 

Pressure elfects on the electronic and structural properties of molecules. ... 

Vibrational spectroscopy is an important probe used to determine the bonding and structural properties of molecules. Powerful techniques such as electron energy loss spectroscopy (EELS) have been developed, which allow one to obtain the vibrational properties of molecules chemisorbed upon surfaces. Due to low concentration, the highly reactive nature of the clusters, and the large number of possible species which are typically present in the cluster beams used to date, unconventional techniques are required in order to obtain spectroscopic information. One unconventional but powerful technique, infrared multiple photon dissociation (IRMPD), has recently been applied to the study of the vibrational properties of gas-phase metal clusters upon which one or more molecules have been chemisorbed. This same technique, IRMPD, has previously been used to obtain the vibrational spectra of ions, species for which it is difficult to apply conventional absorption techniques. 

In this chapter, only QSAR methods which use physicochemical or structural properties of molecules will be discussed, while in Chapter 29 so-called 3D-QSAR approaches will be presented. 3D-QSAR techniques, for example, comparative molecular field analysis (CoMEA), commonly... 

Johannes Hunger (Chapter 7) takes on another of the standard topics in the philosophy of science, explanation. Hunger examines, in detail, various ways that chemists explain and predict the structural properties of molecules. We learn about ab initio methods, empirical force field models and neural network models, each of which have been used to explain and predict molecular structure. And we learn that none of these approaches can be subsumed under either hypothetico-deductive or causal models of explanation. Either chemistry does not offer proper explanations (the normative option) or our philosophical models for explanation are inadequate to cover explanation in chemistry (the descriptive option). Hunger takes the descriptive option and sketches a more pragmatic approach to the explanation that develops Bas van Fraassen s approach to explanation for chemistry. Once again, we find that the philosophy of science has much to learn from the philosophy of chemistry. 

Ultraviolet, infrared and Raman spectroscopy have been used widely to study the modes of vibration - and therefore the structural properties - of molecules. These methods have provided invaluable information for many small clusters in the gas phase, particularly diatomic molecules [14]. There are also very precise data on some larger elemental clusters with symmetrical structures (an example is tetrahedral P [15]), and recent Raman spectroscopy measurements on Si, clusters (n = 4,6,7) [16] have confirmed the predictions of HF-based calculations [17]. Nevertheless, the application to larger clusters in the gas phase has not been widespread to date. One reason has certainly been the difficulty in performing reliable calculations for comparison purposes. 

The values of the elements of atomic polar tensors as evaluated from q. (4.12) depend on die choice of a reference Cartesian coordinate system. Applications in describing structural properties of molecules require to tabulate atomic polar tensor elements for different atoms in various molecular environments. With values depending... 

Dykstra C E 1988 Ab initio Calculation of the Structures and Properties of Molecules (Amsterdam Elsevier)... 

Computational solid-state physics and chemistry are vibrant areas of research. The all-electron methods for high-accuracy electronic stnicture calculations mentioned in section B3.2.3.2 are in active development, and with PAW, an efficient new all-electron method has recently been introduced. Ever more powerfiil computers enable more detailed predictions on systems of increasing size. At the same time, new, more complex materials require methods that are able to describe their large unit cells and diverse atomic make-up. Here, the new orbital-free DFT method may lead the way. More powerful teclmiques are also necessary for the accurate treatment of surfaces and their interaction with atoms and, possibly complex, molecules. Combined with recent progress in embedding theory, these developments make possible increasingly sophisticated predictions of the quantum structural properties of solids and solid surfaces. 

There are a number of properties of molecules that are additive to a reasonable approximation, i.e. the value of such a property of a given molecule is an approximate sum of the values of the properties of either the atoms or bonds present. It has been shown that the dielectric constant is related to some additive properties and it is thus possible to make some estimate of dielectric properties from consideration of molecular structure. 

Up to this point, we have emphasized the stereochemical properties of molecules as objects, without concern for processes which affect the molecular shape. The term dynamic stereochemistry applies to die topology of processes which effect a structural change. The cases that are most important in organic chemistry are chemical reactions, conformational changes, and noncovalent complex formation. In order to understand the stereochemical aspects of a dynamic process, it is essential not only that the stereochemical relationship between starting and product states be established, but also that the spatial features of proposed intermediates and transition states must account for the observed stereochemical transformations. 

Molecular mechanics simulations use the laws of classical physics to predict the structures and properties of molecules. Molecular mechanics methods are available in many computer programs, including MM3, HyperChem, Quanta, Sybyl, and Alchemy. There are many different molecular mechanics methods. Each one is characterized by its particular/orce eW. A force field has these components ... 

An alternative form of the right-handed double helix is A-DNA. A-DNA molecules differ in a number of ways from B-DNA. The pitch, or distance required to complete one helical turn, is different. In B-DNA, it is 3.4 nm, whereas in A-DNA it is 2.46 nm. One turn in A-DNA requires 11 bp to complete. Depending on local sequence, 10 to 10.6 bp define one helical turn in B-form DNA. In A-DNA, the base pairs are no longer nearly perpendicular to the helix axis but instead are tilted 19° with respect to this axis. Successive base pairs occur every 0.23 nm along the axis, as opposed to 0.332 nm in B-DNA. The B-form of DNA is thus longer and thinner than the short, squat A-form, which has its base pairs displaced around, rather than centered on, the helix axis. Figure 12.13 shows the relevant structural characteristics of the A- and B-forms of DNA. (Z-DNA, another form of DNA to be discussed shortly, is also depicted in Figure 12.13.) A comparison of the structural properties of A-, B-, and Z-DNA is summarized in Table 12.1. 

On the other hand, it has also become clear that a materials-oriented synthesis of conjugated poly(phenylene)s cannot narrow its attention to properties of molecules only in solution, but has to include aspects of processing and supramolecu-lar ordering as well. The rigid-rod character of PPPs therefore suggests the use of chain stiffness as a structure-forming principle in the design of supramolecular motifs. 

While there is much to discuss about order in films of different conjugated molecules, a comprehensive survey of the structural properties of various conjugated polymers can be found in Ref. [9]. This section focuses on the relation between microscopic order and macroscopic properties, and on structure-property relations. 

Molecular orbital calculations, whether by ab initio or semiempirical methods, can be used to obtain structures (bond distances and angles), energies (such as heats of formation), dipole moments, ionization energies, and other properties of molecules, ions, and radicals—not only of stable ones, but also of those so unstable that these properties cannot be obtained from experimental measurements." Many of these calculations have been performed on transition states (p. 279) this is the only way to get this information, since transition states are not, in general, directly observable. Of course, it is not possible to check data obtained for unstable molecules and transition states against any experimental values, so that the reliability of the various MO methods for these cases is always a question. However, our confidence in them does increase when (1) different MO methods give similar results, and (2) a particular MO method works well for cases that can be checked against experimental methods. ... 

Bacci M (1984) The Role of Vibronic Coupling in the Interpretation of Spectroscopic and Structural Properties of Biomolecules. 55 67-99 Baekelandt BG, Mortier WJ, Schoonheydt RA (1993) The EEM Approach to Chemical Hardness in Molecules and Solids Fundamentals and Applications. 80 187-228 Baker EC, Halstead GW, Raymond KN (1976) The Structure and Bonding of 4/and 5/Series Organometallic Compounds. 25 21-66 Baibas LC, see Alonso JA (1987) 66 41-78 Baibas LC, see Alonso JA (1993) 80 229-258... 

Volkenshtein, M. V., Stroenie i Fizicheskie Svoistva Molekul Structure and Physical Properties of Molecules), Izdatelstvo Akad. Nauk SSSR, Moscow, 1955, Ch. XII.2. 

The state of research on the two classes of acetylenic compounds described in this article, the cyclo[ ]carbons and tetraethynylethene derivatives, differs drastically. The synthesis of bulk quantities of a cyclocarbon remains a fascinating challenge in view of the expected instability of these compounds. These compounds would represent a fourth allotropic form of carbon, in addition to diamond, graphite, and the fullerenes. The full spectral characterization of macroscopic quantities of cyclo-C should provide a unique experimental calibration for the power of theoretical predictions dealing with the electronic and structural properties of conjugated n-chromophores of substantial size and number of heavy atoms. We believe that access to bulk cyclocarbon quantities will eventually be accomplished by controlled thermal or photochemical cycloreversion reactions of structurally defined, stable precursor molecules similar to those described in this review. 

The purpose of this section is to enable the reader to identify the potential stability properties of a chemical substance by simply analysing its structural formula. This will be made possible by listing the structural properties of unstable molecules. The reader will see the need to identify two types of structural properties those that bear the hallmarks of an unstable property and those whose presence can increase or alternatively reduce the risk of violent decomposition. Since the latter are the only ones in the molecule, they do not represent any danger for it in terms of stability. But when performing qualitative analysis, one also has to take into account the conditions under which the substance is handled. In addition to the structural properties, the analyst will have to carry out a study on the external risk factors. 

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