A supramolecular synthon approach to aid the discovery of architectures sustained by C–H⋯M hydrogen bonds

2013 ◽  
Vol 49 (76) ◽  
pp. 8501 ◽  
Author(s):  
Kafeel Ahmad Siddiqui ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Supramolecular Synthon

The hydrogen-bonded complex bis(tert-butylammonium) 2,6-dichlorophenolate 2,4-dichlorophenol–2,4-dichlorophenolate tetrahydrofuran disolvate containing a chiralR53(10) hydrogen-bonded ring as a supramolecular synthon

2016 ◽  
Vol 72 (10) ◽  
pp. 720-723 ◽  
Author(s):  
Xiao-Qing Cai ◽  
Bei Tian ◽  
Jian-Nan Zhang ◽  
Zhi-Min Jin
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Functional Groups ◽  
High Probability ◽  
Internal Symmetry ◽  
Supramolecular Synthon ◽  
Π Interactions ◽  
Graph Set ◽  
Hydrogen Bonded

A fixed hydrogen-bonding motif with a high probability of occurring when appropriate functional groups are involved is described as a `supramolecular hydrogen-bonding synthon'. The identification of these synthons may enable the prediction of accurate crystal structures. The rare chiral hydrogen-bonding motifR53(10) was observed previously in a cocrystal of 2,4,6-trichlorophenol, 2,4-dichlorophenol and dicyclohexylamine. In the title solvated salt, 2C4H12N+·C6H3Cl2O−·(C6H3Cl2O−·C6H4Cl2O)·2C4H8O, five components, namely twotert-butylammonium cations, one 2,4-dichlorophenol molecule, one 2,4-dichlorophenolate anion and one 2,6-dichlorophenolate anion, are bound by N—H...O and O—H...O hydrogen bonds to form a hydrogen-bonded ring, with the graph-set motifR53(10), which is further associated with two pendant tetrahydrofuran molecules by N—H...O hydrogen bonds. The hydrogen-bonded ring has internal symmetry, with a twofold axis running through the centre of the 2,6-dichlorophenolate anion, and is isostructural with a previous and related structure formed from 2,4-dichlorophenol, dicyclohexylamine and 2,4,6-trichlorophenol. In the title crystal, helical columns are built by the alignment and twisting of the chiral hydrogen-bonded rings, along and across thecaxis, and successive pairs of rings are associated with each other through C—H...π interactions. Neighbouring helical columns are inversely related and, therefore, no chirality is sustained, in contrast to the previous case.

scholarly journals Molecular recognition motifs in cytidinium and 2'-deoxycytidinium salts with composite anions.

1998 ◽  
Vol 45 (4) ◽  
pp. 917-928
Author(s):  
M Gilski ◽  
M Jaskólski
Keyword(s):  
Hydrogen Bond ◽  
Molecular Recognition ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Supramolecular Synthon ◽  
Protonation Site ◽  
Recognition Pattern ◽  
Recognition Motifs

In the crystal structures of N3-protonated cytidinium and 2'-deoxycytidinium salts with composite XYn anions capable of accepting hydrogen bonds through their Y atoms, the dominating motif of cytosinium...anion interactions consists of a pair of hydrogen bonds donated from the N3+ -H protonation site and from the exoamino N4-H41 group cis to N3, and accepted by two Y centers of one anion. This multipoint recognition pattern is stable and robust and thus can be classified as a supramolecular synthon. In a broader group of N3-protonated, N1-substituted cytosinium salts with composite anions it occurs with 70% frequency. The C5 side of the cytosine ring mimics the N3+ -H type synthon and shows a propensity to form an analogous motif in which a C5-H5...Y hydrogen bond replaces the strong N3+ -H...Y interaction. Since the C-H...Y bond is much weaker, the secondary motif shows higher deformability and is less frequent (44%).

scholarly journals Binding motif of ebselen in solution: chalcogen and hydrogen bonds team up

2020 ◽  
Vol 44 (47) ◽  
pp. 20697-20703
Author(s):  
Andrea Daolio ◽  
Patrick Scilabra ◽  
Maria Enrica Di Pietro ◽  
Chiara Resnati ◽  
Kari Rissanen ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Binding Motif ◽  
Supramolecular Synthon ◽  
Chalcogen Bond

Ebselen, a compound active against SARS-CoV-2, forms a bifurcated supramolecular synthon thanks to chalcogen bond and hydrogen bond cooperation.

4,4′-Bipyridine-1,1′-diium acetylenedicarboxylate: a new member of the (H2bipy)[Cu(ox)2] (bipy is 4,4′-bipyridine and ox is oxalate) family

2015 ◽  
Vol 71 (5) ◽  
pp. 357-362 ◽  
Author(s):  
Xiaocui Chen ◽  
Yue Wang ◽  
Shumin Han ◽  
Yongju Wei ◽  
Ruiyao Wang
Keyword(s):  
Hydrogen Bonds ◽  
Structure Type ◽  
Dimensional Structure ◽  
Supramolecular Synthon ◽  
One Dimensional ◽  
Cell Parameters ◽  
Π Interactions ◽  
Weak Intermolecular Interactions ◽  
Similar Unit ◽  
Multiple Interactions

4,4′-Bipyridine-1,1′-diium (H2bipy) acetylenedicarboxylate, C10H12N22+·C4O42−, (1), is a new member of a family of related structures with similar unit-cell parameters. The structures in this family reported previously [Chenet al.(2012).CrystEngComm,14, 6400–6403] are (H2bipy)[Cu(ox)2] (ox is oxalate), (2), (H2bipy)[NaH(ox)2], (3), and (H2bipy)[H2(ox)2], (4). Compound (1) has a one-dimensional structure, in which H2bipy2+cations and acetylenedicarboxylate (ADC2−) anions are linked through a typical supramolecular synthon,i.e.R22(7), and form linear `–cation–anion–' ribbons. Through an array of nonclassical C—H...O hydrogen bonds, adjacent ribbons interact to give two-dimensional sheets. These sheets stack to form a layered structureviaπ–π interactions between the H2bipy2+cations of neighbouring layers. The supramolecular isostructurality of compounds (1)–(4) is ascribed to the synergistic effect of multiple interactions in these structures. The balanced strong and weak intermolecular interactions stabilizing this structure type include strong charge-assisted N—H...O hydrogen bonds, C—H...O contacts and π–π interactions.

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>

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