Variations in Complementary Hydrogen Bonds Direct Assembly Patterns of Isosteric Polyheteroaromatics at Surfaces

2021 ◽  
Author(s):  
David L. Wisman ◽  
Heechan Kim ◽  
Chungryeol Kim ◽  
Tobias W. Morris ◽  
Dongwhan Lee ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Direct Assembly

Use of molecular overlap to predict intermolecular repulsion in N... H-O hydrogen bonds

1998 ◽  
Vol 95 (3) ◽  
pp. 525-537 ◽  
Author(s):  
I. NOBELI S. L. PRICE R. J. WHEATLEY
Keyword(s):  
Hydrogen Bonds

On symmetrical O-H-O hydrogen bonds

1964 ◽  
Vol 25 (5) ◽  
pp. 487-492 ◽  
Author(s):  
R.E. Rundle
Keyword(s):  
Hydrogen Bonds

A Crystallographic Study of Bis[S-benzyl-5-bromo-2-oxoindolin-3-ylidenemethanehydrazonthioate] Disulfide Solvated with Dimethylsulfoxide

2012 ◽  
Vol 9 (2) ◽  
pp. 87
Author(s):  
Mohd Abdul Fatah Abdul Manan ◽  
M. Ibrahim M. Tahir ◽  
Karen A. Crouse ◽  
Fiona N.-F. How ◽  
David J. Watkin
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Solvent Molecule ◽  
Site Occupancy ◽  
Unit Cell Parameters ◽  
Intermolecular Hydrogen Bonds ◽  
Triclinic Space Group ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Thiol Form

The crystal structure of the title compound has been determined. The compound crystallized in the triclinic space group P -1, Z = 2, V = 1839 .42( 18) A3 and unit cell parameters a= 11. 0460( 6) A, b = 13 .3180(7) A, c=13. 7321 (8) A, a = 80.659(3 )0, b = 69 .800(3 )0 and g = 77 .007 (2)0 with one disordered dimethylsulfoxide solvent molecule with the sulfur and oxygen atoms are distributed over two sites; S101/S102 [site occupancy factors: 0.6035/0.3965] and 0130/0131 [site occupancy factor 0.3965/0.6035]. The C22-S2 l and C 19-S20 bond distances of 1. 779(7) A and 1. 788(8) A indicate that both of the molecules are connected by the disulfide bond [S20-S21 2.055(2) A] in its thiol form. The crystal structure reveals that both of the 5-bromoisatin moieties are trans with respect to the [S21-S20 and CI 9-Nl 8] and [S20-S21 and C22-N23] bonds whereas the benzyl group from the dithiocarbazate are in the cis configuration with respect to [S21-S20 and C19-S44] and [S20-S21 and C22-S36] bonds. The crystal structure is further stabilized by intermolecular hydrogen bonds of N9-H35···O16 formed between the two molecules and N28-H281 ···O130, N28-H281 ···O131 and C4 l-H4 l l ···O 131 with the solvent molecule.

Molecular Characterization of the Surface Excess Charge Layer in Droplets

2020 ◽  
Author(s):  
Victor Kwan ◽  
Styliani Consta
Keyword(s):  
Hydrogen Bonds ◽  
Surface Charge ◽  
Droplet Size ◽  
Chloride Ions ◽  
Total Charge ◽  
Excess Charge ◽  
Surface Excess ◽  
High Concentration ◽  
Dipole Orientation ◽  
Charge Layer

<div>Charged droplets play a central role in native mass spectrometry, atmospheric aerosols and in serving as micro-reactors for accelerating chemical reactions. The surface excess charge layer in droplets has often been associated with distinct chemistry. Using molecular simulations for droplets with Na+ and Cl- ions we have found that this layer is ≈ 1.5−1.7 nm thick and depending on the droplet size it includes 33%-55% of the total number of ions. Here, we examine the effect of droplet size and nature of ions in the structure of the surface excess charge layer by using molecular dynamics. We find that in the presence of simple ions the thickness of the surface excess charge layer is invariant not only with respect to droplet size but also with respect to the nature of the simple ions and it is not sensitive to fine details of different force fields used in our simulations.</div><div> In the presence of macroions the excess surface charge layer may extend to 2.0. nm. For the same droplet size, iodide and model hydronium ions show considerably higher concentration than the sodium and chloride ions. <br></div><div>We also find that differences in the average water dipole orientation in the presence of cations and anions in this layer are reflected in the charge distributions. Within the surface charge layer, the number of hydrogen bonds reduces gradually relative to the droplet interior where the number of hydrogen bonds is on the average 2.9 for droplets of diameter < 4 nm and 3.5 for larger droplets. The decrease in the number of hydrogen bonds from the interior to the surface is less pronounced in larger droplets. In droplets with diameter < 4 nm and high concentration of ions the charge of the ions is not compensated only by the solvent polarization charge but by the total charge that also includes the other free charge. This finding shows exceptions to the commonly made assumption that the solvent compensates the charge of the ions in solvents with very high dielectric constant. The study provides molecular insight into the bi-layer droplet structure assumed in the equilibrium partitioning model of C. Enke and assesses critical assumptions of the Iribarne-Thomson model for the ion-evaporation mechanism. <br></div>

Macrocycles of Higher Ortho-Phenylenes: Assembly and Folding

2019 ◽  
Author(s):  
Zacharias Kinney ◽  
Viraj Kirinda ◽  
Scott Hartley
Keyword(s):  
Chemical Shift ◽  
Higher Order ◽  
Order Structure ◽  
Complex Geometries ◽  
Spatial Relationships ◽  
Predominant Species ◽  
Bite Angle ◽  
Direct Assembly

<p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p>

Macrocycles of Higher ortho-Phenylenes: Assembly and Folding

2019 ◽  
Author(s):  
Zacharias Kinney ◽  
Viraj Kirinda ◽  
Scott Hartley
Keyword(s):  
Chemical Shift ◽  
Higher Order ◽  
Order Structure ◽  
Complex Geometries ◽  
Spatial Relationships ◽  
Predominant Species ◽  
Bite Angle ◽  
Direct Assembly

<p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p>

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