Experimental Study of Molecular Structure

Minimization of electrostatic interactions as defined by the various parameters described above, was done in order to calculate bond angles in halomethanes, -silanes and -germanes, as well as one-centre compounds that contain lone pairs and double bonds. The comparison with experimental values is such as to leave no doubt about the power of the VSEPR model. 

Molecular structure is traditionally analyzed [176] by the methods of either diffraction, spectroscopy or ab initio calculation. 

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In the last decade two-dimensional (2D) layers at surfaces have become an interesting field of research [13-27]. Many experimental studies of molecular adsorption have been done on metals [28-40], graphite [41-46], and other substrates [47-58]. The adsorbate particles experience intermolecular forces as well as forces due to the surface. The structure of the adsorbate is determined by the interplay of these forces as well as by the coverage (density of the adsorbate) and the temperature and pressure of the system. In consequence a variety of superstructures on the surfaces have been found experimentally [47-58], a typical example being the a/3 x a/3- structure of adsorbates on a graphite structure (see Fig. 1). 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

Electron Transfer (ET) is a basic chemical process and is the fundamental step in oxidation-reduction reactions. Therefore it can be found in organic chemistry, inorganic chemistry, material science and biochemistry. The study of the structure and reactivity of radical ions, the primary species formed upon electron transfer of parent closed-shell systems, has been a topic of interest for several years. Initially, the research in this field focused on the experimental exploration of molecular structures in terms of their hyperfine structure. However, the interest has shifted during the past decade to the mechanistic studies of these reactive intermediates. 

Experimental studies of the structures of metal alkoxides started more than 40 years ago. The very first study of this kind was made at Moscow State University in 1957 by Struchkov and Lobanova and was devoted to the investigation of W(OPh)6 [1358], During the last 20 years work in the field of structural studies of metal alkoxides and phenoxides has been intensified. At present more than 1000 structures of the derivatives containing exclusively OAlk- and OAr- functional groups have been described. We consider them in relation to their molecular complexity beginning with the monomers and finishing with polymers. ... 

About 25 years ago experimental and theoretical studies of molecular structures and conformational properties were done quite separately. Because theoretical methods have also become applicable for reasonably sized molecules, experimental investigators started to take advantage of these methods and included molecular mechanics (MM), semi-empirical, and later ab initio and/or density flmctional (DFT) calculations in their experimental analyses. Today, because computer programs are very easy to use and sufficient computer capacity is generally available, most experimental studies of gas phase structures by gas electron diffraction (GED), microwave (MW), or high-resolution infrared spectroscopy are combined with theoretical calculations. 

Anharmonicity of molecular vibrations presents one of the most vexing problems in studies of molecular structure. Anharmonic corrections (of first order, involving the cubic force constants) are required in accurate determinations of the equilibrium structures of molecules from rotational spectra, as well as from electron diffraction measurements. To obtain accurate harmonic force fields, it is necessary first to correct the vibrational data for anharmonicity (using second-order corrections, involving cubic and quartic force constants). Information on anharmonic force fields obtained from experimental data is also important as a basis for comparison in quantum chemical investigations of molecular forces as well as in studies of high-temperature thermodynamic properties and of rate and dissociation processes. Yet detailed studies of anharmonic force fields have hitherto been limited to small molecules with N = 2-4 atoms (in isolated cases to N = 6). 

Mixtures of polymer chain belonging to the same chemical species but with different isotopic compositions (deuterated and non-deuterated) have been widely used for experimental studies of polymer structures, since good neutron beams became available. This technique, combining the preparation of adequate samples and neutron scattering experiments, enabled the experimentalists to determine the size of polymer chains (polystyrene or polydimethylsiloxane), in all kinds of polymer mixtures or concentrated polymer solutions. However, the technique relies on the fact that the deuterated and non-deuterated isotopic varieties of a same polymer are compatible with one another. It is admitted that under the experimental conditions described above, the mixture constitutes a unique phase. In fact, the mixing energy of deuterated and non-deuterated chains is probably very small. However, it is non-zero, in particular, because of differences in atomic volumes and polarizabilities. Thus, there is no doubt that demixtion may occur in mixtures of deuterated and undeuterated chains of very high molecular masses. 

Our approach to this chapter is best described as experimental rather than mathematical. There are many excellent formal texts, some of which will be cited. Here, we wish to summarize the fundamental purpose of each technique, to explore its possible applications and limitations, and to illustrate (or provide references to) its use in systematic studies of molecular structure. Most of the examples have been drawn from the Cambridge Structural Database [2], using the methods of search and retrieval detailed in the preceding chapter. We preface the statistical content with two more general chemical sections in the first we discuss the selection of geometric parameters that are most appropriate for certain types of analysis, whilst in the second we discuss the possible sources of variation in crystallographic structural data. 

Vibrational spectroscopy has been applied to the study of molecular structure and physical properties of conjugated polyfurans <92CPL(l9l)419, 93JCP(98)769, 93SM(57)4467>. Vibrational spectra provide simultaneous and selective information on the structure of a polymer and on its charge distribution. Interpretation of experimental data is performed with the assistance of lattice dynamics calculations. 

Information obtainable from experimental determination of molecular structure in other phases than those mentioned above is severely limited for two reasons the scarcity of available means except for the NMR technique, and the complications arising from heterogeneous environments. Recent intensive interest in the structure of molecules forming monolayers or other types of aggregates absorbed on the surface spur exploration of new methods for observing surface structures such as scanning tunneling microscope (STM). Dynamic structural aspects obtainable from these studies are, however, outside of this review. ... 

The historical development of the experimental procedures began with the examination of molecules in the crystalline state, principally with the aid of x-rays. Here the early work following Max von Laue s fundamental discovery should be cited, particularly that of W. H. and W. L. Bragg and of P. Debye and P. Scherrer, while in subsequent years and up to the present day a great number of eminent research workers have contributed to this field. After the proof by Davisson and Germer and by G. P. Thomson of the wave nature of electrons in rapid motion, this technique was also applied to the study of molecular structure in the crystalline state. ... 

Just as the study of molecular structure has benefited from new experimental and theoretical developments, mechanistic studies of complex chemical reactions. 

The power of magnetic resonance techniques to elucidate structure and bonding has been well established in the half century since the development of nuclear magnetic resonance. This paper reviews studies of molecular structure and molecular dynamics, all in the solid state, for a few principal energetic materials. In addition to traditional NMR methods, the principal experimental technique used is nuclear quadrupole resonance (NQR), chosen because it enables observation of high resolution spectra rich in structural information, even for polycrystalline or amorphous materials . ... 

The investigation of PCSs was based upon the theoretical prerequisites of the conjugation concept. This concept, developed on the basis of theoretical analysis and experimental studies of the properties of compounds with low molecular weights, has played an essential role in the progress of our understanding of the nature of the chemical bond, structure, and the reactivity of substances. 

Our discussion concentrates on experimental information providing some insight into the difficulties and limitations of these studies. In places, results from quantum chemical calculations will be invoked for comparison however, a critical analysis of the application of these methods to sulfones and sulfoxides is beyond the scope of this section. As in previous reviews in this series3,6,7, we shall be concerned primarily with the geometrical aspects of molecular structures. 

A question of practical interest is the amount of electrolyte adsorbed into nanostructures and how this depends on various surface and solution parameters. The equilibrium concentration of ions inside porous structures will affect the applications, such as ion exchange resins and membranes, containment of nuclear wastes [67], and battery materials [68]. Experimental studies of electrosorption studies on a single planar electrode were reported [69]. Studies on porous structures are difficult, since most structures are ill defined with a wide distribution of pore sizes and surface charges. Only rough estimates of the average number of fixed charges and pore sizes were reported [70-73]. Molecular simulations of nonelectrolyte adsorption into nanopores were widely reported [58]. The confinement effect can lead to abnormalities of lowered critical points and compressed two-phase envelope [74]. 

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