Halogen bonding versus hydrogen bonding induced 2D self-assembled nanostructures at the liquid–solid interface revealed by STM

The reaction of bipyridine with hydroiodic acid in the presence of iodine gave two new polyiodide-containing salts best described as 4,4´-bipyridinium bis(triiodide), C10H10N2[I3]2, 1, and bis(4,4´-bipyridinium) diiodide bis(triiodide) tris(diiodine) solvate dihydrate, (C10H10N2)2I2[I3]2 · 3 I2 ·2H2O, 2. Both compounds have been structurally characterized by crystallographic and spectroscopic methods (Raman and IR). Compound 1 is composed of I3 − anions forming one-dimensional polymers connected by interionic halogen bonds. These chains run along [101] with one crystallographically independent triiodide anion aligned and the other triiodide anion perpendicular to the chain direction. There are no classical hydrogen bonds present in 1. The structure of 2 consists of a complex I144− anion, 4,4´-bipyridinium dications and hydrogen-bonded water molecules in the ratio of 1 : 2 : 2. The I144− polyiodide anion is best described as an adduct of two iodide and two triiodide anions and three diiodine molecules. Two 4,4´-bipyridinium cations and two water molecules form a cyclic dimer through N-H· · ·O hydrogen bonds. Only weak hydrogen bonding is found between these cyclic dimers and the polyiodide anions.

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Strategies for Crystal Engineering of Polar Solids

MRS Proceedings ◽

10.1557/proc-328-107 ◽

1993 ◽

Vol 328 ◽

Cited By ~ 3

Author(s):

Mike Zaworotko ◽

S. Subramanian ◽

L. R. Macgillivray

Keyword(s):

Hydrogen Bonding ◽

Hydrogen Bonds ◽

Crystal Engineering ◽

Organic Cation ◽

Polar Materials ◽

Structural Analogues ◽

Cubane Cluster ◽

Self Assembled ◽

Hydrogen Bonded

ABSTRACTCrystal engineering has been invoked to design structural analogues of two prototypal SHG active solids, p-nitroaniline (pNA) and potassium dihydrogenphosphate (KDP). pNA exists as linear polar strands because of head-to-tail hydrogen bonding between adjacent molecules whereas KDP is a self-assembled hydrogen bonded diamondoid network that becomes polar when the hydrogen bonds align. We detail preparation and crystallographic characterization of two classes of multicomponent solid, organic cation hydrogen sulfates and cocrystals of the cubane cluster [M (CO)3(μ3-OH)]4, which structurally mimic pNA and KDP, respectively. Several of the Multi-component solids are polar and they represent a generic approach to designing new polar materials since one component can be changed without altering the basic architecture within the crystal.

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Halogen Bonds Fabricate 2D Molecular Self-Assembled Nanostructures by Scanning Tunneling Microscopy

Crystals ◽

10.3390/cryst10111057 ◽

2020 ◽

Vol 10 (11) ◽

pp. 1057

Author(s):

Yi Wang ◽

Xinrui Miao ◽

Wenli Deng

Keyword(s):

Scanning Tunneling Microscopy ◽

Self Assembly ◽

Density Functional ◽

Deep Understanding ◽

Halogen Bonding ◽

The Self ◽

Scanning Tunneling ◽

Halogen Bonds ◽

Tunneling Microscopy ◽

Self Assembled

Halogen bonds are currently new noncovalent interactions due to their moderate strength and high directionality, which are widely investigated in crystal engineering. The study about supramolecular two-dimensional architectures on solid surfaces fabricated by halogen bonding has been performed recently. Scanning tunneling microscopy (STM) has the advantages of realizing in situ, real-time, and atomic-level characterization. Our group has carried out molecular self-assembly induced by halogen bonds at the liquid–solid interface for about ten years. In this review, we mainly describe the concept and history of halogen bonding and the progress in the self-assembly of halogen-based organic molecules at the liquid/graphite interface in our laboratory. Our focus is mainly on (1) the effect of position, number, and type of halogen substituent on the formation of nanostructures; (2) the competition and cooperation of the halogen bond and the hydrogen bond; (3) solution concentration and solvent effects on the molecular assembly; and (4) a deep understanding of the self-assembled mechanism by density functional theory (DFT) calculations.

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Polysulfonylamine, CLXXXV. Wasserstoffbrücken oder Halogenbrücken? Die supramolekularen Strukturen von 3-Bromanilinium- und 4-Bromanilinium-di(4-brombenzolsulfonyl)amid / Polysulfonylamines, CLXXXV. Hydrogen Bonding or Halogen Bonding? The Supramolecular Structures of 3-Bromoanilinium and 4-Bromoanilinium Di(4-bromobenzenesulfonyl)amides

Zeitschrift für Naturforschung B ◽

10.1515/znb-2008-0806 ◽

2008 ◽

Vol 63 (8) ◽

pp. 954-962 ◽

Cited By ~ 3

Author(s):

Virginia Lozano ◽

Matthias Freytag ◽

Peter G. Jones ◽

Armand Blaschette

Keyword(s):

Hydrogen Bonding ◽

Hydrogen Bonds ◽

Halogen Bonding ◽

Database Search ◽

Type I ◽

Two Dimensional ◽

Chemical Difference ◽

One Dimensional ◽

Phenyl Rings ◽

And Inversion

This study characterizes the supramolecular synthons that dominate the interionic organization of 3-bromoanilinium di(4-bromobenzenesulfonyl)amide (1) and the corresponding 4-bromoanilinium salt (2) in their respective crystal structures (1: orthorhombic, Pbca, Z´ = 1; 2: monoclinic, P21/n, Z´ = 1). Although these compounds contain N+-H donors and C-Br groups in equal numbers, their ion packings are exclusively governed by classical, and mostly bifurcated, hydrogen bonds of the type N+-H···O=S/N−, whereas halogen bonding C-Br···O=S/N− is absent from both structures. The isomerism of the cations, which is the only chemical difference between 1 and 2, drives the hydrogen bonds to form a network that is two-dimensional in 1, but one-dimensional in 2. The resulting layers or strands are coherently built up from hydrophilic internal regions consisting of NH3 + and (SO2)2N− groups, external hydrophobic domains of phenyl rings, and peripherically projecting bromine atoms. As the hydrophobic groups from adjacent layers or strands do not interdigitate, the bromine atoms are sterically available to form short Br・・・Br interlayer contacts of quasi-type I in 1 and inversion symmetric Br4 interstrand quadrilaterals in 2. The results of a database search for quadrilateral (C-Br)4 synthons are also presented.

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Use of Pyrazole Hydrogen Bonding in Tripodal Complexes to Form Self Assembled Homochiral Dimers

Materials ◽

10.3390/ma13071595 ◽

2020 ◽

Vol 13 (7) ◽

pp. 1595

Author(s):

Greg Brewer ◽

Raymond J. Butcher ◽

Peter Zavalij

Keyword(s):

Hydrogen Bonding ◽

Hydrogen Bonds ◽

New Materials ◽

Tripodal Ligand ◽

Space Group ◽

Aerial Oxidation ◽

Self Assembled

The 3:1 condensation of 5-methyl-1H-pyrazole-3-carboxaldehyde (MepyrzH) with tris(2-aminoethyl)amine (tren) gives the tripodal ligand tren(MePyrzH)3. Aerial oxidation of a solution of cobalt(II) with this ligand in the presence of base results in the isolation of the insoluble Co(tren)(MePyrz)3. This complex reacts with acids, HCl/NaClO4, NH4ClO4, NH4BF4, and NH4I to give the crystalline compounds Co(tren)(MePyrzH)3(ClO4)3, {[Co(tren)(MePyrzH0.5)3](ClO4)1.5}2 {[Co(tren)(MePyrzH0.5)3](BF4)1.5}2 and [Co(tren)(MePyrzH)3][Co(tren)(MePyrzH)3]I2. The latter three complexes are dimeric, held together by three Npyrazole –H…Npyrazolate hydrogen bonds. The structures and symmetries of these homochiral dimers or pseudodimers are discussed in terms of their space group. Possible applications of these complexes by incorporation into new materials are mentioned.

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N-(4-Bromophenyl)methoxycarbothioamide

Molbank ◽

10.3390/m1012 ◽

2018 ◽

Vol 2018 (3) ◽

pp. M1012

Author(s):

Chien Yeo ◽

Edward Tiekink

Keyword(s):

Molecular Structure ◽

Hydrogen Bonding ◽

Hydrogen Bonds ◽

Title Compound ◽

Molecular Conformation ◽

Three Dimensional ◽

Halogen Bonding ◽

Asymmetric Unit ◽

Weak Intermolecular Interactions ◽

Independent Molecules

The synthesis, spectroscopic and crystallographic characterisation of the title compound, O-methyl-N-4-bromophenyl thiocarbamate, MeOC(=S)N(H)PhBr-4 (1), are described. Spectroscopy confirmed the formation of the compound and the molecular structure was determined crystallographically. Two independent but chemically similar molecules comprise the asymmetric unit of 1. The C‒S and C‒N bond lengths confirm the presence of the thioamide tautomer. The thione-S and amide-N‒H atoms are syn, enabling the formation of amide-N‒H…S(thione) hydrogen bonds between the two independent molecules that generates a two-molecule aggregate via an eight-membered {…HNCS}2 synthon. The aggregates are connected into a three-dimensional architecture via weak intermolecular interactions, including Br…π(4-bromophenyl), S…π(4-bromophenyl), and weak Br…S halogen bonding contacts. The overall molecular conformation, thioamide tautomer, and the presence of amide-N‒H…S(thione) hydrogen bonding in the crystal conform with expectation for this class of compound.

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Structural flexibility of halogen bonds showed in a single-crystal-to-single-crystal [2+2] photodimerization

IUCrJ ◽

10.1107/s2052252518007583 ◽

2018 ◽

Vol 5 (4) ◽

pp. 491-496 ◽

Cited By ~ 19

Author(s):

Michael A. Sinnwell ◽

Jared N. Blad ◽

Logan R. Thomas ◽

Leonard R. MacGillivray

Keyword(s):

Hydrogen Bonds ◽

Single Crystal ◽

Halogen Bonding ◽

Solid State Reactions ◽

Structural Flexibility ◽

Halogen Bonds ◽

Bonded Materials ◽

Limited Opportunity ◽

Structural Database ◽

Geometric Changes

Halogen bonds have emerged as noncovalent forces that govern the assembly of molecules in organic solids with a degree of reliability akin to hydrogen bonds. Although the structure-directing roles of halogen bonds are often compared to hydrogen bonds, general knowledge concerning the fundamental structural behavior of halogen bonds has had limited opportunity to develop. Following an investigation of solid-state reactions involving organic syntheses and the development of photoresponsive materials, this work demonstrates the ability of the components of intermolecular N...I halogen bonding – a `workhorse' interaction for the crystal engineer – to support a single-crystal-to-single-crystal [2+2] photodimerization. A comparison is provided of the geometric changes experienced by the halogen-bonded components in the single-crystal reaction to the current crystal landscape of N...I halogen bonds, as derived from the Cambridge Structural Database. Specifically, a linear-to-bent type of deformation of the halogen-bonded components was observed, which is expected to support the development of functional halogen-bonded materials containing molecules that can undergo movements in close-packed crystal environments.

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Cocrystals of 6-chlorouracil and 6-chloro-3-methyluracil: exploring their hydrogen-bond-based synthon motifs with several triazine and pyrimidine derivatives

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520615003790 ◽

2015 ◽

Vol 71 (2) ◽

pp. 209-220 ◽

Cited By ~ 10

Author(s):

Valeska Gerhardt ◽

Ernst Egert

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonding ◽

Hydrogen Bonds ◽

Crystal Packing ◽

Two Dimensional ◽

Halogen Bonds ◽

Methyl Derivative ◽

Pyrimidine Derivatives ◽

Triazine Derivatives ◽

Solvent Molecules

In order to obtain complexes held together by hydrogen as well as halogen bonds, 6-chlorouracil [6-chloropyrimidin-2,4(1H,3H)-dione; 6CU] and its 3-methyl derivative [6-chloro-3-methylpyrimidin-2,4(1H,3H)-dione; M6CU] were cocrystallized with 2,4,6-triaminopyrimidine and the three triazine derivatives 2,4,6-triamino-1,3,5-triazine (melamine), 2,4-diamino-6-methyl-1,3,5-triazine and 2-chloro-4,6-diamino-1,3,5-triazine, which all offer complementary hydrogen-bonding sites. Three of these compounds form cocrystals with 6CU; however, melamine yielded only a new pseudopolymorph with 6CU, but formed a cocrystal with M6CU. All six cocrystals contain solvent molecules (N,N-dimethylformamide,N,N-dimethylacetamide orN-methylpyrrolidin-2-one), whose intermolecular interactions contribute significantly to the stabilization of the crystal packing. Each of these structures comprises chains, which are primarily formed by strong hydrogen bonds with a basic framework built byR22(8) hydrogen bonds of either pure N—H...N or mixed patterns. Solvent molecules are aligned to the border of these chainsviaN—H...O hydrogen bonds. Two of the reported crystal structures containing 6CU show additional Cl...O halogen bonds, which connect the chains to two-dimensional layers, while one weak and one strong Cl...Cl interaction are observed in the two structures in which molecules of M6CU are present.

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Halogen bonding controlled 2D self-assembled polymorphism of regioisomeric thienophenanthrene derivatives by coadsorption

New Journal of Chemistry ◽

10.1039/d1nj00203a ◽

2021 ◽

Author(s):

Peng Pang ◽

Yi Wang ◽

Xinrui Miao ◽

Bang Li ◽

Wenli Deng

Keyword(s):

Hydrogen Bonding ◽

Formation Mechanism ◽

Self Assembly ◽

Halogen Bond ◽

Bond Formation ◽

Halogen Bonding ◽

Supramolecular Assemblies ◽

The Self ◽

Self Assembled

Deeply understanding the halogen-bond formation mechanism in surface-supported supramolecular assemblies is under explored compared with the existing knowledge of hydrogen bonding. Here we report the self-assembly of regioisomeric bromine substituted...

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