A classification of hydrogen-bonding solvents by sonic velocity measurements

1970 ◽  
Vol 14 (7) ◽  
pp. 1755-1765 ◽  
Author(s):  
J. Kenneth Craver
Keyword(s):  
Hydrogen Bonding ◽  
Sonic Velocity ◽  
Velocity Measurements

Structural systematics of 4,4′-disubstituted benzenesulfonamidobenzenes. 1. Overview and dimer-based isostructures

2007 ◽  
Vol 63 (4) ◽  
pp. 621-632 ◽  
Author(s):  
Thomas Gelbrich ◽  
Michael B. Hursthouse ◽  
Terence L. Threlfall
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Triple Bond ◽  
Common Type ◽  
Dimensional Structure ◽  
One Dimensional ◽  
Distinct Structure ◽  
Polymorphic Forms ◽  
A Chain

One hundred 4,4′-disubstituted benzenesulfonamidobenzenes, X–C6H5–SO2–NH–C6H5–Y, where X, Y = NO2, CN, CF3, I, Br, Cl, F, H, Me, OMe, have been synthesized and their crystal structures determined. The resulting set of 133 structures, which includes polymorphic forms, is used to make a comparative study of the molecular packing and the nature of the intermolecular interactions, including the formation of hydrogen-bonding motifs and the influence of the two substituents X and Y on these features. Nine distinct supramolecular connectivity motifs of hydrogen bonding are encountered. There are 74% of all the structures investigated which exhibit one of two motifs based on N—H...O=S interactions, a dimer or a chain. There are three other, infrequent motifs, also employing N—H...O=S links, which exhibit more complexity. Four different chain motifs result from either N—H...O=N, N—H...C[triple-bond]N or N—H...OMe interactions, arising from the presence of a nitro (position Y), nitrile (X or Y) or methoxy (Y) substituent. The program XPac [Gelbrich & Hursthouse (2005). CrystEngComm, 7, 324–336] was used to systematically analyse the packing relationships between crystal structures. Similar discrete (zero-dimensional) and extended (one-dimensional and two-dimensional) structure components, as well as cases of isostructurality were identified. A hierarchy for the classification of the 56 distinct structure types of this set is presented. The most common type, a series of 22 isostructures containing the simple centrosymmetric N—H...O=S-bonded dimer, is discussed in detail.

scholarly journals Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: Crystal structure analysis, classification, optimal structures and accurate interaction energies

2019 ◽  
Author(s):  
Preethi S. Prabhakar ◽  
Purshotam Sharma ◽  
Abhijit Mitra
Keyword(s):  
Hydrogen Bonding ◽  
Visual Inspection ◽  
Weak Interactions ◽  
Binding Pocket ◽  
Crystal Structure Analysis ◽  
Thiamine Pyrophosphate ◽  
Interaction Energies ◽  
Binding Pockets ◽  
Pairing Interactions

ABSTRACTIn the present work, sixty-seven crystal structures of the aptamer domains of RNA riboswitches, are chosen for analysis of the structure and strength of hydrogen bonding (pairing) interactions between nucleobases constituting the aptamer binding pockets and the bound ligands. A total of eighty unique base:ligand hydrogen-bonded pairs containing at least two hydrogen bonds were identified through visual inspection. Classification of these contacts in terms of the interacting edge of the aptamer nucleobase revealed that interactions involving the Watson-Crick edge are the most common, followed by the sugar edge of purines and the Hoogsteen edge of uracil. Alternatively, classification in terms of the chemical constitution of the ligand yields five unique classes of base:ligand pairs: base:base, base:amino acid, base:sugar, base:phosphate and base:other. Further, quantum mechanical (QM) geometry optimizations revealed that sixty seven out of eighty pairs exhibit stable geometries and optimal deviations from their macromolecular crystal occurrences. This indicates that these contacts are well-defined RNA aptamer:ligand interaction motifs. QM calculated interaction energies of base:ligand pairs reveal rich hydrogen bonding landscape, ranging from weak interactions (base:other, –3 kcal/mol) to strong (base:phosphate, –48 kcal/mol) contacts. The analysis was further extended to study the biological importance of base:ligand interactions in the binding pocket of the tetrahydrofolate riboswitch and thiamine pyrophosphate riboswitch. Overall, our study helps in understanding the structural and energetic features of base:ligand pairs in riboswitches, which could aid in developing meaningful hypotheses in context of RNA:ligand recognition. This can, in turn contribute towards current efforts to develop antimicrobials that target RNAs.

Topological analysis of the electron density in hydrogen bonds

1999 ◽  
Vol 55 (4) ◽  
pp. 563-572 ◽  
Author(s):  
E. Espinosa ◽  
M. Souhassou ◽  
H. Lachekar ◽  
C. Lecomte
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Positive Curvature ◽  
Topological Analysis ◽  
Peptide Bonds ◽  
X Ray ◽  
Systematic Relationships ◽  
Experimental Electron Density

Topological analysis of the experimental electron density ρ(r) in hydrogen-bonding regions has been carried out for a large number of organic compounds using different multipole models and techniques. Relevant systematic relationships between topological properties at the critical points and the usual geometric parameters are pointed out. Results involving X-ray data only and joint X-ray and neutron data, as well as special hydrogen bonding cases (symmetric, bifurcated, peptide bonds, etc.) are included and analysed in the same framework. A new classification of hydrogen bonds using the positive curvature of the electron density at the critical point [\lambda_3({\bf r}_{\rm CP})] is proposed.

Sonic Velocity Measurements in Study of Liquid and Liquid Solution Properties

1955 ◽  
Vol 47 (6) ◽  
pp. 1181-1182 ◽  
Author(s):  
F. C. Collins ◽  
M. H. Navidi ◽  
L. P. Friedman
Keyword(s):  
Liquid Solution ◽  
Sonic Velocity ◽  
Solution Properties ◽  
Velocity Measurements
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