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Run ADS in the standard simplification mode (Save Simplified Net/Standard), but with the option “Contract Atom” under the tab “Topology” checked.ħ. Repeat this procedure, choose “Compound – Auto Determine – Bond Midpoints” again.Ħ. Go to “Compound – Auto Determine – Bond Midpoints”. Now we can create the augmented variant within ToposPro.ĥ. Copy the entry of choice (here reo ) from the “idealnets.cmp” into the newly created database. Even if the coordinates of the augmented version of a net is not in your database “idealnets.cmp”, it is very likely that the coordinates of the basic net are available in the ToposPro database “idealnets.cmp”.ģ. But, if the net from which you want to make a nice-looking figure is present, proceed with step # 15.Ģ. 3000 nets, within ToposPro and look-up, if you can find the desired net. Open this database, which contains approx. There are two possible sources:Ī) RCSR (please checkmark the “including augmented version” option) – for reo the search is unsuccessfullī) ToposPro is delivered with a database called “idealnets.cmp” (search with your File Explorer to find this file). the space group of the net and the fractional coordinates of the nodes. In general, you need the structural information of the net-a net, i.e. In this tutorial we want to make an image of the net reo-a.ġ. Although the gorgeous freeware VESTA has also some capabilities in that respect it is, unfortunately, not suitable. Two of the most frequently used (commercial) packages for this purpose are Diamond and CrystalMaker. #CRYSTALMAKER STRUCTURE SHOWING BONDS SOFTWARE#There is one requisite in order to be able to create and make great looking images of augmented nets: A software package that has the option to make and show customizable coordination polyhedra. A 64, 112–122.Making beautiful pictures of beautiful nets in augmented version Web of Science CrossRef IUCr Journals Google Scholar CrossRef CAS Web of Science Google Scholar Huff, A., Chang, C., Cooper, D., Smith, K. CSD CrossRef CAS Web of Science Google Scholar CrossRef Google Scholarįan, C., Li, G., Zhu, D. CrystalMaker Software Ltd, Oxford, England. Google ScholarĬrystalMaker Software (2009). Bruker AXS Inc., Madison, Wisconsin, USA. CrossRef CAS Web of Science Google Scholarīruker (2011). Web of Science CSD CrossRef CAS IUCr Journals Google Scholarīauman, J. Web of Science CSD CrossRef CAS IUCr Journals Google ScholarĪllen, F. For the use of the title compound in the synthesis of biological compounds, see: Darby et al. For the use of imidazole-containing compounds in coordination chemistry, see: Huff et al. For related structures, see: Nyamori et al. 3).įor background information on imidazole complex formation, see: Bauman & Wang (1964) Fan et al. Hydrogen bonding also takes place between the oxygen (O1") on the hydroxyl group of one molecule and the hydrogen (H2) bonded to a nitrogen (N2) on the imidazole ring of a corresponding molecule. The compound forms hydrogen bonds of 1.985 (8) Å between the nitrogen (N1) on the imidazole ring of one molecule and the hydrogen (H1') of the hydroxyl on an adjacent molecule (Fig. The bond lengths and bond angles are within normal ranges in the molecular structure of this compound (Fig. Here we report on a new imidazole compound, the hydroxymethyl-substituted imidazole, the title compound, C 4H 6N 2O. Histidine, an essential amino acid, and histamine, a bioorganic compound that acts as neurotransmitter, both involve (1 H-imidazol-5-yl)methanol in their respective synthesizes (Darby et al., 1942). A few examples of imidazole complex compounds with biological applications have been reported (Bauman and Wang, 1964). Imidazole-containing metal complexes have a variety of applications, such as redox mediators in enzyme-based electrochemical sensors (Fan et al., 2000). These successes can be attributed to how the nitrogen in imidazole assists in the formation of metal complexes (Fujita et al., 1994). Imidazole ligands have been used in coordination chemistry with great success over the last twenty years (Huff et al., 1993). |
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