scholarly journals Accurate Reproduction of 161 Small-Molecule Complex Crystal Structures using the EUDOC Program: Expanding the Use of EUDOC to Supramolecular Chemistry

PLoS ONE ◽  
2007 ◽  
Vol 2 (6) ◽  
pp. e531 ◽  
Author(s):  
Qi Wang ◽  
Yuan-Ping Pang
2016 ◽  
Vol 69 (11-13) ◽  
pp. 2015-2023 ◽  
Author(s):  
Shaikh M. Mobin ◽  
Mohd. Tauqeer ◽  
Akbar Mohammad ◽  
Veenu Mishra ◽  
Pratibha Kumari

2016 ◽  
Vol 12 ◽  
pp. 125-138 ◽  
Author(s):  
Steven C Zimmerman

This review summarizes part of the author’s research in the area of supramolecular chemistry, beginning with his early life influences and early career efforts in molecular recognition, especially molecular tweezers. Although designed to complex DNA, these hosts proved more applicable to the field of host–guest chemistry. This early experience and interest in intercalation ultimately led to the current efforts to develop small molecule therapeutic agents for myotonic dystrophy using a rational design approach that heavily relies on principles of supramolecular chemistry. How this work was influenced by that of others in the field and the evolution of each area of research is highlighted with selected examples.


I shall concentrate upon reviewing the important recent change in our appreciation of the facts of supercooling which has been brought about particularly by the work of Turnbull at the General Electric Research Laboratory in Schenectady. I suppose that most of us, talking about supercooling a couple of years ago, would have divided substances into two classes, one with simple crystal structures like gold, and all the other ‘good’ metals on the one hand, and those with complex crystal structures, such as glycerol and the silicates on the other; saying that whereas the latter class can be very much supercooled, and will form glasses, the former class can only be supercooled a very few degrees. Then we would have added that there are some ‘ bad ’ metals, with moderately complex crystal structures, such as antimony or bismuth, which can be supercooled some tens of degrees, forming an intermediate class. I think we would then have added that this is quite comprehensible. In particular, that the X-ray diffraction patterns of the monatomic liquids show us that most of the atoms have the right numbers of nearest neighbours in a first co-ordination shell, all ready in place to start the growth of a crystal; which readily explains why these substances cannot be supercooled very much—a nice simple experimental fact, with a straightforward theoretical interpretation—and both are wrong.


Author(s):  
John A. Tossell ◽  
David J. Vaughan

The early descriptions of chemical bonding in minerals and geological materials utilized purely ionic models. Crystals were regarded as being made up of charged atoms or ions that could be represented by spheres of a particular radius. Based on interatomic distances obtained from the early work on crystal structures, ionic radii were calculated for the alkali halides (Wasastjerna, 1923) and then for many elements of geochemical interest by Goldschmidt (1926). Modifications to these radius values by Pauling (1927), and others took account of such factors as different coordination numbers and their effects on radii. The widespread adoption of ionic models by geochemists resulted both from the simplicity and ease of application of these models and from the success of rules based upon them. Pauling’s rules (1929) enabled the complex crystal structures of mineral groups such as the silicates to be understood and to a limited extent be predicted; Goldschmidt’s rules (1937) to some degree enabled the distribution of elements between mineral phases or mineral and melt to be understood and predicted. Such rules are further discussed in later chapters. Ionic approaches have also been used more recently in attempts to simulate the structures of complex solids, a topic discussed in detail in Chapter 3. Chemical bonding theory has, of course, been an important component of geochemistry and mineralogy since their inception. Any field with a base of experimental data as broad as that of mineralogy is critically dependent upon theory to give order to the data and to suggest priorities for the accumulation of new data. Just as the bond with predominantly ionic character was the first to be quantitatively understood within solidstate science, the ionic bonding model was the first used to interpret mineral properties. Indeed, modern studies described herein indicate that structural and energetic properties of some minerals may be adequately understood using this model. However, there are numerous indications that an ionic model is inadequate to explain many mineral properties. It also appears that some properties that may be rationalized within an ionic model may also be rationalized assuming other limiting bond types.


2020 ◽  
Vol 48 (15) ◽  
pp. 8302-8319
Author(s):  
Małgorzata Katarzyna Cabaj ◽  
Paulina Maria Dominiak

Abstract We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.


2019 ◽  
Vol 104 (7) ◽  
pp. 966-972 ◽  
Author(s):  
J.P. Hirth ◽  
Jian Wang ◽  
Greg Hirth

Abstract A topological model (TM) is presented for the complex crystal structures characteristic of some minerals. We introduce a tractable method for applying the TM to characterize defects in these complex materials. Specifically, we illustrate how structural groups, each with a motif containing multiple atoms, provide lattices and structures that are useful in describing dislocations and disconnections in interfaces. Simplified methods for determining the shuffles that accompany disconnection motion are also described. We illustrate the model for twinning in albite owing to its potential application for constraining the rheological properties of the crust at conditions near the brittle-plastic transition, where plagioclase is a major constituent of common rock types. While deformation twins in plagioclase are often observed in crustal rocks, the interpretation of the stress states at which they form has not advanced. The concept of structural groups makes an analysis of the twinning process easier in complex minerals and explicitly predicts the interface structure of the deformation twins.


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