Atomic structure overview

In this contribution, we will first provide an overview of the nature of the systems and phenomena and the modeling and computational challenge which they represent. In the following two sections we describe calculations of the electronic and atomic structure of the interface and of electron transfer at the interface. In each case we present some details of our own results involving copper-water interfaces and electron transfer from a copper ion in... 

Several recent determinations of the atomic structure, relaxation or reconstructions of clean oxide surfaces will next be described. A quick overview of the characterisation of diverse oxide thin films by GIXS will then be given before concluding on the present and future possibilities of the technique applied to the field of oxide surfaces. 

Research dealing with the atomic structure and charge distribution at crystal surfaces is a modern and fast-developing field. Metal and semiconductor surfaces show many interesting features, and this is certainly also the case for electrochemical interfaces, that is, metal (or semiconductor)/(aqueous) solution interfaces. This section is not intended to give a comprehensive overview of surface and interfacial... 

The second chapter is dedicated to properties and sources of radiation suitable for powder diffraction analysis, and gives an overview of the kinematical theory of diffraction along with its consequences in structure determination. Here, readers learn that the diffraction pattern of a crystal is a transformation of an ordered atomic structure into a reciprocal space rather than a direct image of the former. Diffraction from crystalline matter, specifically from polycrystalline materials is described as a function of crystal symmetry, atomic structure and conditions of the experiment. The chapter ends with a general introduction to numerical techniques enabling the restoration of the three-dimensional distribution of atoms in a lattice by the transformation of the diffraction pattern back into direct space. 

Fig. 1.2 L scanning electron microscope image of cotton rag paper showing interlocking cellulose fibers (magnification 800x, approximately source The Paper Project http //paperproject. org/overview.html) right atomic structure of cellulose (CsHiqOs), source wiMmedia commons...

After this short (and unavoidably selective) overview and introduction we shall now work out the theory of relativistic atomic structure calculations. 

The drawing software comprises a comprehensive collection of standard tools to sketch 2D chemical structures. To specify all its facilities and tools would go far beyond the scope of this overview, but there are some nice features that are very useful for chemists so they are mentioned here briefly. One of these enables the prediction of H and NMR shifts from structures and the correlation of atoms with NMR peaks (Figure 2-127). lUPAC standard names can be generated... 

This chapter has given an overview of the structure and dynamics of lipid and water molecules in membrane systems, viewed with atomic resolution by molecular dynamics simulations of fully hydrated phospholipid bilayers. The calculations have permitted a detailed picture of the solvation of the lipid polar groups to be developed, and this picture has been used to elucidate the molecular origins of the dipole potential. The solvation structure has been discussed in terms of a somewhat arbitrary, but useful, definition of bound and bulk water molecules. 

Because LEED theory was initially developed for close packed clean metal surfaces, these are the most reliably determined surface structures, often leading to 7 p factors below 0.1, which is of the order of the agreement between two experimental sets of 7-V curves. In these circumstances the error bars for the atomic coordinates are as small as 0.01 A, when the total energy range of 7-V curves is large enough (>1500 eV). A good overview of state-of-the-art LEED determinations of the structures of clean metal surfaces, and further references, can be found in two recent articles by Heinz et al. [2.272, 2.273]. 

Ab initio molecular orbital theory is concerned with predicting the properties of atomic and molecular systems. It is based upon the fundamental laws of quantum mechanics and uses a variety of mathematical transformation and approximation techniques to solve the fundamental equations. This appendix provides an introductory overview of the theory underlying ab initio electronic structure methods. The final section provides a similar overview of the theory underlying Density Functional Theory methods. 

In line with the policy of Advances to provide periodic coverage of major developments in physical methodology for the study of carbohydrates, A. Dell (London) here surveys the use of fast-atom-bombardment mass spectrometry in application to carbohydrates. This technique has achieved rapid prominence as the soft ionization technique of choice for structural investigation of complex carbohydrate sequences in biological samples. The author s extensive personal involvement in this field makes her chapter a critical, state-of-the-art overview for the specialist, as well as a valuable primer for the reader unfamiliar with this technique. 

As it was mentioned in Section 9.4.1, 3D structures generated by DG have to be optimized. For this purpose, MD is a well-suited tool. In addition, MD structure calculations can also be performed if no coarse structural model exists. In both cases, pairwise atom distances obtained from NMR measurements are directly used in the MD computations in order to restrain the degrees of motional freedom of defined atoms (rMD Section 9.4.2.4). To make sure that a calculated molecular conformation is rehable, the time-averaged 3D structure must be stable in a free MD run (fMD Sechon 9.4.2.5J where the distance restraints are removed and the molecule is surrounded by expMcit solvent which was also used in the NMR measurement Before both procedures are described in detail the general preparation of an MD run (Section 9.4.2.1), simulations in vacuo (Section 9.4.2.2) and the handling of distance restraints in a MD calculation (Section 9.4.2.3) are treated. Finally, a short overview of the SA technique as a special M D method is given in Sechon 9.4.2.6. 

In addition to looking for data trends in physical property space using PCA and PLS, trends in chemical structure space can be delineated by viewing nonlinear maps (NLM) of two-dimensional structure descriptors such as Unity Fingerprints or topological atom pairs using tools such as Benchware DataMiner [42]. Two-dimensional NLM plots provide an overview of chemical structure space and biological activity/molecular properties are mapped in a 3rd and/or 4th dimension to look for trends in the dataset. 

In this section, a group of related approaches is discussed in which the continuum dielectric description of the microscopic environment is replaced by a more detailed model in which the atomic details of the structure and the dynamics of the microscopic environment are taken into account. These models will be referred to here as coupled DFT/Molecular Mechanics (DFT/MM). For a general overview of coupled ab initio/Molecular Mechanics methods, see the recent reviews by Aquist and Warshel186 and by Gao187. 

The survey of possible structures was given in Chapter 8.31 of CHEC-II(1996) <1996CHEC-II(8)747>. However, a short overview could be useful here. This chapter deals with three main types of bicyclic heterocycles containing two ring junction nitrogen atoms, namely bicyclic 5-5, 5-6, and 6-6 ring fused systems which are depicted in their fully saturated forms as structures 1-3. 

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