scholarly journals Balancing Hydrogen Bonding and van der Waals Interactions in Cyclohexane-Based Bisamide and Bisurea Organogelators†

Langmuir ◽  
2009 ◽  
Vol 25 (15) ◽  
pp. 8802-8809 ◽  
Author(s):  
Niek Zweep ◽  
Andrew Hopkinson ◽  
Auke Meetsma ◽  
Wesley R. Browne ◽  
Ben L. Feringa ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Van Der Waals ◽  
Van Der Waals Interactions

A topological analysis of the interion interactions of tetraphenylphosphonium squarate

2006 ◽  
Vol 84 (5) ◽  
pp. 804-811 ◽  
Author(s):  
David Wolstenholme ◽  
Manuel AS Aquino ◽  
T Stanley Cameron ◽  
Joseph D Ferrara ◽  
Katherine N Robertson
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Critical Points ◽  
Topological Analysis ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Multipole Refinement ◽  
Diverse Interactions

The tetraphenylphosphonium squarate salt crystallizes with a number of diverse interactions, which all have the potential to be classified as hydrogen bonds. The squarate anions are found as dimers linked by O-H···O interactions. The multipole refinement of the tetraphenylphosphonium squarate was performed using the Hansen–Coppens model followed by topological analysis of its intermolecular interactions. A total of 28 interactions were found among the symmetry related molecules, which include a number of C-H···Cπ, C-H···O, and C-H···H-C interactions, along with the O-H···O interaction. With the criteria for hydrogen bonding proposed by Popelier and Koch, it is possible to determine which of these interactions are hydrogen bonds and which are van der Waals interactions. Both linear and exponentially dependent correlations can be seen for the properties of the bond critical points involving the intermolecular interactions that fulfill these criteria. All this leads to a better understanding of the role that hydrogen bonds play in the formation of small organic compounds.Key words: electron density, multiple refinement, hydrogen bonds.

Competition and cooperativity of hydrogen-bonding and tetrel-bonding interactions involving triethylene diamine (DABCO), H2O and CO2 in air

2020 ◽  
Vol 44 (6) ◽  
pp. 2328-2338 ◽  
Author(s):  
Jianming Yang ◽  
Qinwei Yu ◽  
Fang-Ling Yang ◽  
Ka Lu ◽  
Chao-Xian Yan ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Tetrel Bond

Triethylene diamine (DABCO) can interact with H2O and CO2 in air to form dimeric and trimeric complexes via hydrogen bond, tetrel bond as well as van der Waals interactions.

MMPEP: Development and evaluation of peptide parameters for Allinger's MMP2(85) programme, including calculations on crambin and insulin

1988 ◽  
Vol 66 (11) ◽  
pp. 2687-2702 ◽  
Author(s):  
Saul Wolfe ◽  
Donald Fredric Weaver ◽  
Kiyull Yang
Keyword(s):  
Hydrogen Bonding ◽  
Force Field ◽  
Van Der Waals ◽  
Heavy Atom ◽  
Van Der Waals Interactions ◽  
Heavy Atoms ◽  
Minimization Procedure ◽  
Natural Result ◽  
Experimental Crystal ◽  
Initial Starting

Allinger's MMP2(85) program has been converted to an IBM environment, and the dimensions expanded to a current maximum of 999 atoms. Substantial additional expansion will be possible. An all-atom set of parameters, which permit Allinger's comprehensive force field to be applied to the molecular mechanics treatment of peptides, has been determined. These parameters, termed MMPEP, contain 21 atom types: 5 for carbon, 6 for hydrogen, 5 for nitrogen, 4 for oxygen, and 1 for sulfur, and are based on crystallographic heavy atom bond lengths and bond angles, vibrational and microwave spectra, and ab initio calculations. To minimize the conformational energy of a peptide from an initial starting geometry, all internally stored parameters are released, and replaced by PEPCON, a 360-line external file containing the MMPEP parameters.The ability of the MMPEP parameterization of MM85 to reproduce experimental crystal structures has been tested on several peptides and polypeptides, and the use of a dielectric constant ε = 78.5 D leads to the following results: Ala-Ala-Gly (rms = 0.261); Gly-Gly-Val (rms = 0.349); glutathione (rms = 0.417); crambin (327 heavy atoms; rms = 0.310 for all heavy atoms); insulin (389 heavy atoms; rms = 0.646 for all heavy atoms); the origins of deviations can be interpreted. No problems have been encountered in the application of the Newton–Raphson minimization procedure to such large molecules as crambin and insulin, even though all possible nonbonded interactions have been retained. On the IBM 3081 computer, real time minimization of trip)eptides requires 1–2 min, crambin requires 250 min, and insulin 200 min. Since hydrogen bonding in Allinger's force field is a natural result of electrostatic and van der Waals interactions, in MMPEP hydrogen bonding is taken into account through the large number of hydrogen atom types and their different bond moments and van der Waals radii.

scholarly journals Crystal structure and halogen–hydrogen bonding of a Delépine reaction intermediate

2021 ◽  
Vol 77 (1) ◽  
pp. 1-4
Author(s):  
David Z. T. Mulrooney ◽  
Helge Müller-Bunz ◽  
Tony D. Keene
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Van Der Waals ◽  
Hirshfeld Surface ◽  
Van Der Waals Interactions ◽  
Hirshfeld Surface Analysis ◽  
Space Group ◽  
Molecular Salt

The reaction of 1,5-dibromopentane with urotropine results in crystals of the title molecular salt, 5-bromourotropinium bromide [systematic name: 1-(5-bromopentyl)-3,5,7-triaza-1-azoniatricyclo[3.3.1.13,7]decane bromide], C11H22BrN4 +·Br− (1), crystallizing in space group P21/n. The packing in compound 1 is directed mainly by H...H van der Waals interactions and C—H...Br hydrogen bonds, as revealed by Hirshfeld surface analysis. Comparison with literature examples of alkylurotropinium halides shows that the interactions in 1 are consistent with those in other bromides and simple chloride and iodide species.

Hydrogen-Bonding versus van der Waals Interactions in Self-Assembled Monolayers of Substituted Isophthalic Acids

Langmuir ◽  
2010 ◽  
Vol 26 (23) ◽  
pp. 18155-18161 ◽  
Author(s):  
Pearl N. Dickerson ◽  
Amber M. Hibberd ◽  
Nuri Oncel ◽  
Steven L. Bernasek
Keyword(s):  
Hydrogen Bonding ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Self Assembled Monolayers ◽  
Assembled Monolayers ◽  
Self Assembled
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