Complexes of HArF and AuX (X = F, Cl, Br, I). Comparison of H‐bonds, halogen bonds, F‐shared bonds and covalent bonds

Diversity of mutual orientations of Y–S and I–X and covalent bonds in molecular crystals complicate categorizing noncovalent chalcogen and halogen bonds. Here, the different types of S...I interactions with short interatomic distances are analysed. The selection of S...I interactions for the categorization of the chalcogen and halogen bonds has been made using angles that determine the mutual orientation of electron lone pairs and σ-holes interacted S and I atoms. In complicated cases of noncovalent interactions with `hole-to-hole' of S and I orientations, distinguishing the chalcogen and halogen bonds is only possible if the atom is uniquely determined, which also provides the electrophilic site. The electronic criterion for chalcogen/halogen bonds categorizing that is based on analysis of dispositions of electron density and electrostatic potential minima along the interatomic lines has been suggested and its effectiveness has been demonstrated.

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Synthesis of an extended halogen-bonded metal–organic structure in a one-pot mechanochemical reaction that combines covalent bonding, coordination chemistry and supramolecular synthesis

CrystEngComm ◽

10.1039/c4ce01815j ◽

2014 ◽

Vol 16 (44) ◽

pp. 10169-10172 ◽

Cited By ~ 34

Author(s):

Dominik Cinčić ◽

Tomislav Friščić

Keyword(s):

Coordination Chemistry ◽

Covalent Bonding ◽

Mechanochemical Reaction ◽

Halogen Bonds ◽

One Pot ◽

Covalent Bonds ◽

Extended Structure ◽

Organic Structure ◽

Metal Organic ◽

Coordination Bonds

We describe a four-component one-pot mechanochemical reaction which combines the formation of covalent bonds, coordination bonds and halogen bonds to obtain an extended structure based on halogen-bonded metal–organic units.

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Halogen bonding in hypervalent iodine and bromine derivatives: halonium salts

IUCrJ ◽

10.1107/s2052252517004262 ◽

2017 ◽

Vol 4 (4) ◽

pp. 411-419 ◽

Cited By ~ 30

Author(s):

Gabriella Cavallo ◽

Jane S. Murray ◽

Peter Politzer ◽

Tullio Pilati ◽

Maurizio Ursini ◽

...

Keyword(s):

Halogen Bonding ◽

Electron Donors ◽

Hypervalent Iodine ◽

Halogen Bonds ◽

Covalent Bonds ◽

Ionic Compounds ◽

Short Contacts

Halogen bonds have been identified in a series of ionic compounds involving bromonium and iodonium cations and several different anions, some also containing hypervalent atoms. The hypervalent bromine and iodine atoms in the examined compounds are found to have positive σ-holes on the extensions of their covalent bonds, while the hypervalent atoms in the anions have negative σ-holes. The positive σ-holes on the halogens of the studied halonium salts determine the linearity of the short contacts between the halogen and neutral or anionic electron donors, as usual in halogen bonds.

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Variations of quantum electronic pressure under the external compression in crystals with halogen bonds assembled in Cl3-, Br3-, I3-synthons

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520620006113 ◽

2020 ◽

Vol 76 (4) ◽

pp. 514-523

Author(s):

Ekaterina Bartashevich ◽

Sergey Sobalev ◽

Yury Matveychuk ◽

Vladimir Tsirelson

Keyword(s):

Electron Density ◽

Stacking Interactions ◽

Structural Elements ◽

Halogen Bonds ◽

External Compression ◽

Covalent Bonds ◽

Quantum Electronic ◽

Electronic Pressure

The inner-crystal quantum electronic pressure was estimated for unstrained C6Cl6, C6Br6, and C6I6 crystals and for those under external compression simulated from 1 to 20 GPa. The changes in its distribution were analyzed for the main structural elements in considered crystals: for triangles of the typical halogen bonds assembled in Hal3-synthons, where Hal = Cl, Br, I; for Hal...Hal stacking interactions, as well as for covalent bonds. Under simulated external compression, the quantum electronic pressure in the intermolecular space reduces as the electron density increases, indicating spatial areas of relatively less crystal resistance to external compression. The most compliant C6Cl6 crystal shows the largest changes of quantum electronic pressure in the centre of Cl3-synthon while the deformation of rigid I3-synthon under external compression depends only on the features of I...I halogen bonds.

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Temperature Dependence of the Critical Electron Dose for Fatty Acid Monolayers

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100053188 ◽

1982 ◽

Vol 40 ◽

pp. 78-79

Author(s):

Kenneth H. Downing ◽

Robert M. Glaeser

Keyword(s):

Electron Beam ◽

Fatty Acid ◽

Inelastic Scattering ◽

Temperature Dependence ◽

Structural Damage ◽

Direct Result ◽

Second Step ◽

Strong Temperature Dependence ◽

Electron Dose ◽

Covalent Bonds

The structural damage of molecules irradiated by electrons is generally considered to occur in two steps. The direct result of inelastic scattering events is the disruption of covalent bonds. Following changes in bond structure, movement of the constituent atoms produces permanent distortions of the molecules. Since at least the second step should show a strong temperature dependence, it was to be expected that cooling a specimen should extend its lifetime in the electron beam. This result has been found in a large number of experiments, but the degree to which cooling the specimen enhances its resistance to radiation damage has been found to vary widely with specimen types.

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Structural Transformation of a Germanium Σ=13 (510) [001] Tilt Grain Boundary under the Electron Beam

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100179014 ◽

1990 ◽

Vol 48 (1) ◽

pp. 52-53 ◽

Cited By ~ 1

Author(s):

Jean-Luc Rouvière ◽

Alain Bourret

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

Grain Boundary ◽

Structural Transformation ◽

Mirror Symmetry ◽

High Resolution Electron Microscopy ◽

Structural Transformations ◽

Covalent Bonds ◽

Resolution Electron ◽

Tilt Grain Boundary

The possible structural transformations during the sample preparations and the sample observations are important issues in electron microscopy. Several publications of High Resolution Electron Microscopy (HREM) have reported that structural transformations and evaporation of the thin parts of a specimen could happen in the microscope. Diffusion and preferential etchings could also occur during the sample preparation.Here we report a structural transformation of a germanium Σ=13 (510) [001] tilt grain boundary that occurred in a medium-voltage electron microscopy (JEOL 400KV).Among the different (001) tilt grain boundaries whose atomic structures were entirely determined by High Resolution Electron Microscopy (Σ = 5(310), Σ = 13 (320), Σ = 13 (510), Σ = 65 (1130), Σ = 25 (710) and Σ = 41 (910), the Σ = 13 (510) interface is the most interesting. It exhibits two kinds of structures. One of them, the M-structure, has tetracoordinated covalent bonds and is periodic (fig. 1). The other, the U-structure, is also tetracoordinated but is not strictly periodic (fig. 2). It is composed of a periodically repeated constant part that separates variable cores where some atoms can have several stable positions. The M-structure has a mirror glide symmetry. At Scherzer defocus, its HREM images have characteristic groups of three big white dots that are distributed on alternatively facing right and left arcs (fig. 1). The (001) projection of the U-structure has an apparent mirror symmetry, the portions of good coincidence zones (“perfect crystal structure”) regularly separate the variable cores regions (fig. 2).

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Imine Based Self-Healing Hydrogel Triggered by Periodate

10.26434/chemrxiv.12592322 ◽

2020 ◽

Author(s):

Alexis Wolfel ◽

Cecilia Inés Alvarez Igarzabal ◽

Marcelo Ricardo Romero

Keyword(s):

Functional Groups ◽

Time Window ◽

Crosslinking Reaction ◽

Self Healing ◽

Swelling Properties ◽

Covalent Bonds ◽

Smart Systems ◽

Primary Amino ◽

Vicinal Diols ◽

Aldehyde Groups

<p>Design of materials with novel sensitivities and smart behaviour is important for the development of smart systems with automated responsiveness. We have recently reported the synthesis of hydrogels, cross-linked by <i>N,N'</i>-diallyltartardiamide (DAT). The covalent DAT-crosslinking points have vicinal diols which can be easily cleaved with periodate, generating valuable a-oxo-aldehyde functional groups, useful for further chemical modification. Based on those findings, we envisioned that a self-healable hydrogel could be obtained by incorporation of primary amino functional groups, from <a>2-aminoethyl methacrylate </a>hydrochloride (AEMA), coexisting with DAT into the same network. The a-oxo-aldehyde groups generated after the reaction with periodate would arise in the immediate environment of amine groups to form imine cross-links. For this purpose, DAT-crosslinked hydrogels were synthesized and carefully characterized. The cleavage of DAT-crosslinks with periodate promoted changes in the mechanical and swelling properties of the materials. As expected, a self-healing behavior was observed, based on the spontaneous formation of imine covalent bonds. In addition, we surprisingly found a combination of fast vicinal diols cleavage and a low speed self-crosslinking reaction by imine formation. Consequently, it was found a time-window in which a periodate-treated polymer was obtained in a transient liquid state, which can be exploited to choose the final shape of the material, before automated gelling. The singular properties attained on these hydrogels could be useful for developing sensors, actuators, among other smart systems.</p>

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Seeded Growth of Single-Crystal Two-Dimensional Covalent Organic Frameworks

10.26434/chemrxiv.5702437.v2 ◽

2017 ◽

Cited By ~ 1

Author(s):

Austin M. Evans ◽

Lucas R. Parent ◽

Nathan C. Flanders ◽

Ryan P. Bisbey ◽

Edon Vitaku ◽

...

Keyword(s):

Molecular Transport ◽

Controlled Synthesis ◽

Two Dimensional ◽

Covalent Organic Frameworks ◽

Seeded Growth ◽

Covalent Bonds ◽

Crystalline Materials ◽

Step Procedure ◽

Structures And Properties ◽

2D Polymer

<div> <div> <div> <p>Polymerizing monomers into periodic two-dimensional (2D) networks provides structurally precise, atomically thin macromolecular sheets linked by robust, covalent bonds. These materials exhibit desirable mechanical, optoelectrotronic, and molecular transport properties derived from their designed structure and permanent porosity. 2D covalent organic frameworks (COFs) offer broad monomer scope, but are generally isolated as polycrystalline, insoluble powders with limited processability. Here we overcome this limitation by controlling 2D COF formation using a two- step procedure. In the first step, 2D COF nanoparticle seeds are prepared with approximate diameters of 30 nm. Next, monomers are slowly added to suppress new nucleation while promoting epitaxial growth on the existing seeds to sizes of several microns. The resulting COF nanoparticles are of exceptional and unprecedented quality, isolated as single crystalline materials with micron-scale domain sizes. These findings advance the controlled synthesis of 2D layered COFs and will enable a broad exploration of synthetic 2D polymer structures and properties. </p> </div> </div> </div>

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Seeded Growth of Single-Crystal Two-Dimensional Covalent Organic Frameworks

10.26434/chemrxiv.5702437 ◽

2017 ◽

Author(s):

Austin M. Evans ◽

Lucas R. Parent ◽

Nathan C. Flanders ◽

Ryan P. Bisbey ◽

Edon Vitaku ◽

...

Keyword(s):

Molecular Transport ◽

Controlled Synthesis ◽

Two Dimensional ◽

Covalent Organic Frameworks ◽

Seeded Growth ◽

Covalent Bonds ◽

Crystalline Materials ◽

Step Procedure ◽

Structures And Properties ◽

2D Polymer

<div> <div> <div> <p>Polymerizing monomers into periodic two-dimensional (2D) networks provides structurally precise, atomically thin macromolecular sheets linked by robust, covalent bonds. These materials exhibit desirable mechanical, optoelectrotronic, and molecular transport properties derived from their designed structure and permanent porosity. 2D covalent organic frameworks (COFs) offer broad monomer scope, but are generally isolated as polycrystalline, insoluble powders with limited processability. Here we overcome this limitation by controlling 2D COF formation using a two- step procedure. In the first step, 2D COF nanoparticle seeds are prepared with approximate diameters of 30 nm. Next, monomers are slowly added to suppress new nucleation while promoting epitaxial growth on the existing seeds to sizes of several microns. The resulting COF nanoparticles are of exceptional and unprecedented quality, isolated as single crystalline materials with micron-scale domain sizes. These findings advance the controlled synthesis of 2D layered COFs and will enable a broad exploration of synthetic 2D polymer structures and properties. </p> </div> </div> </div>

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QM/MM Simulations of Organic Phosphorus Adsorption at the Diaspore-Water Interface

10.26434/chemrxiv.8075204 ◽

2019 ◽

Author(s):

Prasanth Babu Ganta ◽

Oliver Kühn ◽

Ashour Ahmed

Keyword(s):

Interaction Energy ◽

Dynamics Simulation ◽

Water Molecules ◽

Hydroxyl Groups ◽

Water Interface ◽

Mineral Surfaces ◽

Soil Mineral ◽

Phosphorus Adsorption ◽

Covalent Bonds ◽

Binding Mechanisms

The phosphorus (P) immobilization and thus its availability for plants are mainly affected by the strong interaction of phosphates with soil components especially soil mineral surfaces. Related reactions have been studied extensively via sorption experiments especially by carrying out adsorption of ortho-phosphate onto Fe-oxide surfaces. But a molecular-level understanding for the P-binding mechanisms at the mineral-water interface is still lacking, especially for forest eco-systems. Therefore, the current contribution provides an investigation of the molecular binding mechanisms for two abundant phosphates in forest soils, inositol hexaphosphate (IHP) and glycerolphosphate (GP), at the diaspore mineral surface. Here a hybrid electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) based molecular dynamics simulation has been applied to explore the diaspore-IHP/GP-water interactions. The results provide evidence for the formation of different P-diaspore binding motifs involving monodentate (M) and bidentate (B) for GP and two (2M) as well as three (3M) monodentate for IHP. The interaction energy results indicated the abundance of the GP B motif compared to the M one. The IHP 3M motif has a higher total interaction energy compared to its 2M motif, but exhibits a lower interaction energy per bond. Compared to GP, IHP exhibited stronger interaction with the surface as well as with water. Water was found to play an important role in controlling these diaspore-IHP/GP-water interactions. The interfacial water molecules form moderately strong H-bonds (HBs) with GP and IHP as well as with the diaspore surface. For all the diaspore-IHP/GP-water complexes, the interaction of water with diaspore exceeds that with the studied phosphates. Furthermore, some water molecules form covalent bonds with diaspore Al atoms while others dissociate at the surface to protons and hydroxyl groups leading to proton transfer processes. Finally, the current results conﬁrm previous experimental conclusions indicating the importance of the number of phosphate groups, HBs, and proton transfers in controlling the P-binding at soil mineral surfaces.

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