Faculty Opinions recommendation of Graphical representation standards for chemical structure diagrams.

Author(s):  
John Proudfoot
2009 ◽  
Vol 81 (6) ◽  
pp. 1131-1186 ◽  
Author(s):  
Máximo Barón ◽  
Karl-Heinz Hellwich ◽  
Michael Hess ◽  
Kazuyuki Horie ◽  
Aubrey D. Jenkins ◽  
...  

This document defines class names of polymers based on the class names of starting monomers and characteristic features of the chemical constitution of polymer molecules (macromolecules), i.e., class names that have gained general acceptance in the polymer and material literature, science and technology as well as in public. The glossary is divided into three parts: Source-based class names, which identify common classes of starting monomers such as "acrylic", "diene", "phenolic", "vinylic". Class names based on chemical structure, which identify characteristic groups in the main chains (backbones) of the polymer molecules such as (i) inter-unit groups derived from functional groups, e.g., "amide", "ester", "ether"; (ii) a specific group of atoms, e.g., "alkenylene", "siloxane", "sulfone"; (iii) ring structures, e.g., "benzimidazole", "benzoxazole", "quinoxaline". Class names based on molecular architecture, which identify mainly the overall shapes of polymer molecules through the type of their graphical representation such as "linear", "branched", "dendritic", "comb". Each part of the glossary is arranged in a non-hierarchical alphabetical order. Each entry provides: (a) the polymer class name; (b) its definition; (c) specific or generic examples including IUPAC names and a structure or graphical representation; (d) relations to other polymer classes and subclasses; (e) notes on the inclusion or exclusion of borderline cases. An alphabetical index of all class names is included.


2007 ◽  
Vol 15 (03) ◽  
pp. 287-297 ◽  
Author(s):  
JIE SONG

A new 3D graphical representation of DNA sequences according to chemical structures of the bases is proposed, reflecting the distribution of bases with different chemical structure, preserving information on sequential adjacency of bases, avoiding loss of information accompanying alternative 3D representations in which the curve standing for DNA overlaps and intersects itself. Based on this representation, a numerical characterization approach is presented by constructing a six-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with the DNA sequences. The examination of similarities among the coding sequences of the first exon of β-globin gene of different species illustrates the utility of the approach.


2008 ◽  
Vol 80 (2) ◽  
pp. 277-410 ◽  
Author(s):  
Jonathan Brecher

The purpose of a chemical structure diagram is to convey information - typically the identity of a molecule - to another human reader or as input to a computer program. Any form of communication, however, requires that all participants understand each other. Recommendations are provided for the display of two-dimensional chemical structure diagrams in ways that avoid ambiguity and are likely to be understood correctly by all viewers. Examples are provided in many areas, ranging from issues of typography and color selection to the relative positioning of portions of a diagram and the rotational alignment of the diagram as a whole. Explanations describe which styles are preferred and which should be avoided. Principal recommendations include: 1) Know your audience: Diagrams that have a wide audience should be drawn as simply as possible; 2) Avoid ambiguous drawing styles; 3) Avoid inconsistent drawing styles.


Author(s):  
J. Silcox

In this introductory paper, my primary concern will be in identifying and outlining the various types of inelastic processes resulting from the interaction of electrons with matter. Elastic processes are understood reasonably well at the present experimental level and can be regarded as giving information on spatial arrangements. We need not consider them here. Inelastic processes do contain information of considerable value which reflect the electronic and chemical structure of the sample. In combination with the spatial resolution of the electron microscope, a unique probe of materials is finally emerging (Hillier 1943, Watanabe 1955, Castaing and Henri 1962, Crewe 1966, Wittry, Ferrier and Cosslett 1969, Isaacson and Johnson 1975, Egerton, Rossouw and Whelan 1976, Kokubo and Iwatsuki 1976, Colliex, Cosslett, Leapman and Trebbia 1977). We first review some scattering terminology by way of background and to identify some of the more interesting and significant features of energy loss electrons and then go on to discuss examples of studies of the type of phenomena encountered. Finally we will comment on some of the experimental factors encountered.


Author(s):  
N.-H. Cho ◽  
K.M. Krishnan ◽  
D.B. Bogy

Diamond-like carbon (DLC) films have attracted much attention due to their useful properties and applications. These properties are quite variable depending on film preparation techniques and conditions, DLC is a metastable state formed from highly non-equilibrium phases during the condensation of ionized particles. The nature of the films is therefore strongly dependent on their particular chemical structures. In this study, electron energy loss spectroscopy (EELS) was used to investigate how the chemical bonding configurations of DLC films vary as a function of sputtering power densities. The electrical resistivity of the films was determined, and related to their chemical structure.DLC films with a thickness of about 300Å were prepared at 0.1, 1.1, 2.1, and 10.0 watts/cm2, respectively, on NaCl substrates by d.c. magnetron sputtering. EEL spectra were obtained from diamond, graphite, and the films using a JEOL 200 CX electron microscope operating at 200 kV. A Gatan parallel EEL spectrometer and a Kevex data aquisition system were used to analyze the energy distribution of transmitted electrons. The electrical resistivity of the films was measured by the four point probe method.


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