scholarly journals Evaluation of covalent-bond density in molecular crystals using simplified virtual scattering centers: inorganic and complex compounds

2020 ◽  
Vol 76 (a1) ◽  
pp. a164-a164
Author(s):  
Alexander Nazarenko
Author(s):  
Michał Kaźmierczak ◽  
Andrzej Katrusiak

The survey of the shortest contacts in structures deposited in the Cambridge Structural Database shows that chalcogen...halogen, halogen...halogen and chalcogen...chalcogen interactions can compete as cohesion forces in molecular crystals. The smallest parameter δ (defined as the interatomic distance minus the sum of relevant van der Waals radii) for Ch...X contacts between chalcogens (Ch: S, Se) and halogens (X: F, Cl, Br, I) is present only in 0.86% out of 30 766 deposited structures containing these atoms. Thus, in less than 1% of these structures can the Ch...X forces be considered as the main type of cohesion forces responsible for the molecular arrangement. Among the 263 structures with the shortest Ch...X contact, there are four crystals where no contacts shorter than the sums of van der Waals radii are present (so-called loose crystals). The smallest δ criterion has been used for distinguishing between the bonding (covalent bond) and non-bonding contacts and for validating the structural models of crystals.


2018 ◽  
Vol 91 (3) ◽  
pp. 343-348 ◽  
Author(s):  
Masato Suzuki ◽  
Takahiro Fujii ◽  
Yoko Naito ◽  
Kazuhisa Yamoto ◽  
Shin-ichi Matsuoka ◽  
...  

Author(s):  
James F. Hainfeld ◽  
Frederic R. Furuya

Glutaraldehyde is a useful tissue and molecular fixing reagents. The aldehyde moiety reacts mainly with primary amino groups to form a Schiff's base, which is reversible but reasonably stable at pH 7; a stable covalent bond may be formed by reduction with, e.g., sodium cyanoborohydride (Fig. 1). The bifunctional glutaraldehyde, (CHO-(CH2)3-CHO), successfully stabilizes protein molecules due to generally plentiful amines on their surface; bovine serum albumin has 60; 59 lysines + 1 α-amino. With some enzymes, catalytic activity after fixing is preserved; with respect to antigens, glutaraldehyde treatment can compromise their recognition by antibodies in some cases. Complicating the chemistry somewhat are the reported side reactions, where glutaraldehyde reacts with other amino acid side chains, cysteine, histidine, and tyrosine. It has also been reported that glutaraldehyde can polymerize in aqueous solution. Newer crosslinkers have been found that are more specific for the amino group, such as the N-hydroxysuccinimide esters, and are commonly preferred for forming conjugates. However, most of these linkers hydrolyze in solution, so that the activity is lost over several hours, whereas the aldehyde group is stable in solution, and may have an advantage of overall efficiency.


Author(s):  
Raja Subramanian ◽  
Kenneth S. Vecchio

The structure of stacking faults and partial dislocations in iron pyrite (FeS2) have been studied using transmission electron microscopy. Pyrite has the NaCl structure in which the sodium ions are replaced by iron and chlorine ions by covalently-bonded pairs of sulfur ions. These sulfur pairs are oriented along the <111> direction. This covalent bond between sulfur atoms is the strongest bond in pyrite with Pa3 space group symmetry. These sulfur pairs are believed to move as a whole during dislocation glide. The lattice structure across these stacking faults is of interest as the presence of these stacking faults has been preliminarily linked to a higher sulfur reactivity in pyrite. Conventional TEM contrast analysis and high resolution lattice imaging of the faulted area in the TEM specimen has been carried out.


Author(s):  
S. Kirchanski ◽  
D. Branton

We have investigated the effect of integral membrane proteins upon the fracturing of frozen lipid bilayers. This investigation has been part of an effort to develop freeze fracture labeling techniques and to assess the possible breakage of covalent protein bonds during the freeze fracture process. We have developed an experimental protocol utilizing lectin affinity columns which should detect small amounts of covalent bond breakage during the fracture of liposomes containing purified (1) glycophorin (a transmembrane glycoprotein of human erythrocyte membranes). To fracture liposomes in bulk, frozen liposomes are ground repeatedly under liquid nitrogen. Failure to detect any significant covalent bond breakage (contrary to (2)) led us to question the effectiveness of our grinding procedure in fracturing and splitting lipid bilayers.


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