Structure Matters

Grandy, A. S., and Neff, J. C. (2008). Molecular C dynamics downstream The biochemical decomposition sequence and its impact on soil organic matter structure and function. Sci. Total Environ. 404(2/3), 297-303. 

This capability of self-assembly to make ordered arrays of nanostructures is, in essence, nothing new. Crystallization of molecular or atomic species (whether it is the phase transition of liquid water into solid ice, or of liquid silicon into semiconductor-grade silicon crystal) is an example of self-assembly, as are the formation of surfactants in soap bubbles126, the crystallization of viruses for x-ray structure determination127, and the ordering of liquid crystals in displays128. The novelty of self-assembly is in the focus on the formation of matter structured rationally at scales less than 100 nm, and the realization that the only practical method of achieving these structure is to have the components assemble themselves spontaneously. 

When talking about difficulties in interpreting experimental evidences for disordered (amorphous) solids, the researchers often plead the lack of the theory of their matter structure. To what questions about the surface structure of amorphous silica might the theory answer ... 

A broader perspective is provided in C. K. Jorgensen and G.B. Kauffman, Crookes and Marignac - A centennial of an intuitive and pragmatic appraisal of chemical elements and the present astrophysical status of nucleosynthesis and dark matter , Structure and Bonding 73 (1990) 227-253. 

Taylor WD, Bae JN, MacFall JR et al. (2007). Widespread effects of hyperintense lesions on cerebral white matter structure. American Journal of Roentgenology 188 1695-1704... 

T. Naumann, H. Matter, Structural classification of protein kinases using 3D molecular interaction field analysis of their ligand binding sites Target family landscapes,/. Med. Chem. 2002, 45, 2366-2378. 

Solid-phase speciation. While most speciation studies have been concerned with redox speciation in solution, speciation in the solid phase is also of interest. Both reduced and oxidized arsenic and selenium species can be adsorbed on minerals, sods, and sediments albeit with differing affinities (see Sections 9.02.5.3 and 9.02.7.2). Such adsorption has been demonstrated on metal oxides and clays and also probably takes place, to some extent, on carbonates, phosphates, sulhdes, and perhaps organic matter. Structural arsenic and selenium may also be characterized. 

Hereafter, we give some examples of optical studies on single molecules which provide new information on condensed matter structure or dynamics. In these experiments, single molecules or single nanoparticles can be considered as probes of their environment. 

According to Maciel [22] "The availability of high-resolution NMR techniques for solids permits the use of NMR as a structure-determination bridge between the solid and liquid states of matter". Structural information is provided which is not available from X-ray diffraction. For decomposition studies, variable temperature facilities are required. Haw [20] has described the problems associated with such measurements, including rotor design and also temperature measurement and control. 

Gess-Newsome, J. Lederman, N.G. (1995). Biology teachers perceptions of subject matter structure and its relationship to classroom practice. Journal of Research in Science Teaching, 32 (3), 301-325. 

The reason for using different radiations to investigate condensed matter structure lies in the different interaction mechanism of neutrons, x-rays and electrons with atoms, that supplies more detailed information on the atomic arrangement and the dynamics of solids. X-Ray scattering of short wavelength (A) electromagnetic radiation is performed by the electronic shell of atoms. The scattering from the nuclei is about 10 times smaller, due to the factor (e /mc ) in the... 

Recently, ab initio or the first-principle molecular dynamics (AIMD), which is based on Car and Parrinello s technique [33], has become a valuable method for study condensed matter structure and dynamics, in particular liquids, surfaces, and clusters. The basic idea underlying AIMD method is to compute the forces acting on the nuclei from electronic structure that are calculated on the fly as the molecular dynamics trajectory is generated [34]. In this way, the electronic variables are not integrated out beforehand, but are considered as active degrees of freedom. Thus, the Car and Parrinello (CP) algorithm overcomes limitations of standard empirical-potential approaches employed in classical molecular dynamics and... 

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