scholarly journals Not Only Hydrogen Bonds: Other Noncovalent Interactions

Crystals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 180 ◽  
Author(s):  
Ibon Alkorta ◽  
José Elguero ◽  
Antonio Frontera
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Periodic Table ◽  
Alkaline Earth ◽  
Noncovalent Interactions ◽  
Priority Rules ◽  
Dissociation Energies ◽  
Group 12 ◽  
Different Types ◽  
Membrane Ion Transport

In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.

Formation and distortion of iodidoantimonates(III): the first isolated [SbI6]3−octahedron

2017 ◽  
Vol 73 (3) ◽  
pp. 432-442 ◽  
Author(s):  
Maciej Bujak
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Structural Parameters ◽  
Hybrid Structure ◽  
Organic Hybrid ◽  
Hydrogen Bond Interactions ◽  
Different Types ◽  
Spatial Dimensions ◽  
Induced Changes

The ability to intentionally construct, through different types of interactions, inorganic–organic hybrid materials with desired properties is the main goal of inorganic crystal engineering. The primary deformation, related to intrinsic interactions within inorganic substructure, and the secondary deformation, mainly caused by the hydrogen bond interactions, are both responsible for polyhedral distortions of halogenidoantimonates(III) with organic cations. The evolution of structural parameters, in particular the Sb—I secondary- and O/N/C—H...I hydrogen bonds, as a function of temperature assists in understanding the contribution of those two distortion factors to the irregularity of [SbI6]3−polyhedra. In tris(piperazine-1,4-diium) bis[hexaiodidoantimonate(III)] pentahydrate, (C4H12N2)3[SbI6]2·5H2O (TPBHP), where the isolated [SbI6]3–units were found, distortion is governed only by O/N/C—H...I hydrogen bonds, whereas in piperazine-1,4-diium bis[tetraiodidoantimonate(III)] tetrahydrate, (C4H12N2)[SbI4]2·4H2O (PBTT), both primary and O—H...I secondary factors cause the deformation of one-dimensional [{SbI4}n]n−chains. The larger in spatial dimensions piperazine-1,4-diium cations, in contrast to the smaller water of crystallization molecules, do not significantly contribute to the octahedral distortion, especially in PBTT. The formation of isolated [SbI6]3−ions in TPBHP is the result of specific second coordination sphere hydrogen bond interactions that stabilize the hybrid structure and simultaneously effectively separate and prevent [SbI6]3−units from mutual interactions. The temperature-induced changes, further supported by the analysis of data retrieved from the Cambridge Structural Database, illustrate the significance of both primary and secondary distortion factors on the deformation of octahedra. Also, a comparison of packing features in the studied hybrids with those in the non-metal containing piperazine-1,4-diium diiodide diiodine (C4H12N2)I2·I2(PDD) confirms the importance and hierarchy of different types of interactions.

Two novel alkaline earth coordination polymers constructed from cinnamic acid and 1,10-phenanthroline: synthesis and structural and thermal properties

2018 ◽  
Vol 74 (2) ◽  
pp. 240-247 ◽  
Author(s):  
Nassima Bendjellal ◽  
Chahrazed Trifa ◽  
Sofiane Bouacida ◽  
Chaouki Boudaren ◽  
Mhamed Boudraa ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Coordination Polymers ◽  
Crystal Engineering ◽  
Alkaline Earth ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
X Ray ◽  
Carboxylate Groups ◽  
A Chain

In coordination chemistry and crystal engineering, many factors influence the construction of coordination polymers and the final frameworks depend greatly on the organic ligands used. The diverse coordination modes of N-donor ligands have been employed to assemble metal–organic frameworks. Carboxylic acid ligands can deprotonate completely or partially when bonding to metal ions and can also act as donors or acceptors of hydrogen bonds; they are thus good candidates for the construction of supramolecular architectures. We synthesized under reflux or hydrothermal conditions two new alkaline earth(II) complexes, namely poly[(1,10-phenanthroline-κ2N,N′)bis(μ-3-phenylprop-2-enoato-κ3O,O′:O)calcium(II)], [Ca(C10H7O2)2(C10H8N2)]n, (1), and poly[(1,10-phenanthroline-κ2N,N′)(μ3-3-phenylprop-2-enoato-κ4O:O,O′:O′)(μ-3-phenylprop-2-enoato-κ3O,O′:O)barium(II)], [Ba(C10H7O2)2(C10H8N2)]n, (2), and characterized them by FT–IR and UV–Vis spectroscopies, thermogravimetric analysis (TGA) and single-crystal X-ray diffraction analysis, as well as by powder X-ray diffraction (PXRD) analysis. Complex (1) features a chain topology of type 2,4 C4, where the Ca atoms are connected by O and N atoms, forming a distorted bicapped trigonal prismatic geometry. Complex (2) displays chains of topology type 2,3,5 C4, where the Ba atom is nine-coordinated by seven O atoms of bridging/chelating carboxylate groups from two cinnamate ligands and by two N atoms from one phenanthroline ligand, forming a distorted tricapped prismatic arrangement. Weak C—H...O hydrogen bonds and π–π stacking interactions between phenanthroline ligands are responsible to the formation of a supramolecular three-dimensional network. The thermal decompositions of (1) and (2) in the temperature range 297–1173 K revealed that they both decompose in three steps and transform to the corresponding metal oxide.

Crystal Engineering Using Bis- and Tris-phenols. Adducts with 1,4,8,11-Tetraazacyclotetradecane (Cyclam): Isolated Ladders in the Adduct with 4,4'-Thiodiphenol, Tethered Ladders in the Adduct with 4,4'-Sulfonyldiphenol and Two Interwoven Three-Dimensional Networks in the Adduct with 1,1,1-Tris(4-hydroxyphenyl)ethane

1998 ◽  
Vol 54 (2) ◽  
pp. 139-150 ◽  
Author(s):  
G. Ferguson ◽  
C. Glidewell ◽  
R. M. Gregson ◽  
P. R. Meehan
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Three Dimensional ◽  
Dimensional Array ◽  
Different Types ◽  
Molecular Components

The structure of 4,4′-thiodiphenol–1,4,8,11-tetraazacyclotetradecane (2/1), (C12H10O2S)2.C10H24N4 (1), monoclinic, P21/c, a = 11.1602 (12), b = 10.8084 (12), c = 14.001 (2) Å, β = 103.127 (10)°, with Z = 2, contains phenolate anions [HOC6H4SC6H4O]− and diprotonated cyclam cations [C10H26N4]2+: these cations have the centrosymmetric trans-III conformation and the two additional protons are contained within the N4 cavity of the macrocycle, held by three-centre hydrogen bonds. The phenolate anions form chains, held together by O—H...O hydrogen bonds, and pairs of these chains are cross-linked into ladders by the [cyclamH2]2+ cations by means of N—H...O hydrogen bonds. The structure of 4,4′-sulfonyldiphenol–1,4,8,11-tetraazacyclotetradecane (2/1), (C12H10O4S)2.C10H24N4 (2), triclinic, P1¯, a = 10.9345 (10), b = 11.0060 (10), c = 14.350 (2) Å, α = 79.532 (10), β = 86.739 (10), γ = 87.471 (10)°, with Z = 2, contains phenolate anions [HOC6H4SO2C6H4O]− and cyclam dications [C10H26N4]2+: the phenolate anions are linked into antiparallel chains, cross-linked by the cyclam cations. There are two distinct types of ladder in the structure running along (0, y, 0) and (1\over2, y, 1\over2), respectively, and these bundled ladders are tied together by C—H...O hydrogen bonds to form a continuous three-dimensional array. In 1,1,1-tris(4-hydroxyphenyl)ethane–1,4,8,11-tetraazacyclotetradecane–methanol (2/1/1), (C20H18O3)2.C10H24N4.CH4O (3), triclinic, P1¯, a = 8.2208 (11), b = 16.245 (2), c = 17.337 (2) Å, α = 81.694 (13), β = 89.656 (14), γ = 86.468 (12)°, with Z = 2, the structure contains centrosymmetric diprotonated cyclam cations of precisely the same type as found in (1), phenolate anions [(HOC6H4)2C(CH3)C6H4O]− and neutral methanol molecules. The molecular components are linked together by nine different types of hydrogen bond, five of O—H...O type and four of N—H...O type, to form chains running in the [001], [010] (two sets), [211] and [211¯] directions. The combination of these chain motifs generates two independent three-dimensional networks which are fully interwoven, but not bonded to one another.

Structure of the Holliday junction: applications beyond recombination

2017 ◽  
Vol 45 (5) ◽  
pp. 1149-1158 ◽  
Author(s):  
P. Shing Ho
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Noncovalent Interactions ◽  
Three Dimensional ◽  
Essential Element ◽  
Dna Origami ◽  
Holliday Junction ◽  
Dna Assembly ◽  
Halogen Bonds ◽  
Sequence Dependence

The Holliday junction (HJ) is an essential element in recombination and related mechanisms. The structure of this four-stranded DNA assembly, which is now well-defined alone and in complex with proteins, has led to its applications in areas well outside of molecular recombination, including nanotechnology and biophysics. This minireview explores some interesting recent research on the HJ, as it has been adapted to design regular two- or three-dimensional lattices for crystal engineering, and more complex systems through DNA origami. In addition, the sequence dependence of the structure is discussed in terms how it can be applied to characterize the geometries and energies of various noncovalent interactions, including halogen bonds in oxidatively damaged (halogenated) bases and hydrogen bonds associated with the epigenetic 5-hydroxylmethylcytosine base.

Statistical analysis of noncovalent interactions of anion groups in crystal structures. I. Hydrogen bonding of sulfate anions

1996 ◽  
Vol 52 (4) ◽  
pp. 677-684 ◽  
Author(s):  
L. Chertanova ◽  
C. Pascard
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Small Molecules ◽  
Crystal Structures ◽  
Noncovalent Interactions ◽  
Data Set ◽  
Hydrogen Bond Acceptor ◽  
Covalently Bonded ◽  
Different Types

The hydrogen-bond acceptor characteristics of sulfate dianions are analyzed in crystal structures of small molecules. For 85 anions, neither coordinated to metal ions nor covalently bonded, 697 hydrogen bonds are faund. Of these, 266 (38%) are the O...H—O type and 431 (62%) are the O...H—N type, proportions that correspond well to the stoichiometry of the compounds studied and indicate no preference for a particular donor. The analysis of the data set, after classifying the hydrogen bonds according to the different types of donors, shows that O...H—O bonds are more linear than O...H—N. The anion oxygen–acceptor function is characterized by multiple hydrogen bonding. Only in 56 cases does a sulfate oxygen participate in a single hydrogen bond. In most cases every sulfate oxygen is coordinated by two (187 cases) or three (89 cases) hydrogen bonds. For three H donors, the preferred coordination geometry of the sulfate oxygen is pyramidal. The most frequent coordination around a sulfate dianion is with eight to ten H donors. Thus, sulfate dianions can play a significant cohesive role in molecular aggregation.

The X40x10 Halogen Bonding Benchmark Revisited: Surprising Importance of (n-1)d Subvalence Correlation

2017 ◽  
Author(s):  
Manoj Kumar Kesharwani ◽  
Nitai Sylvetsky ◽  
Debashree Manna ◽  
Jan M.L. Martin
Keyword(s):  
Dissociation Energy ◽  
Noncovalent Interactions ◽  
Halogen Bonding ◽  
Coupled Cluster ◽  
Dissociation Energies ◽  
Iodine Species ◽  
Explicitly Correlated ◽  
High Level ◽  
Cluster Methods ◽  
Small Separation

<p>We have re-evaluated the X40x10 benchmark for halogen bonding using conventional and explicitly correlated coupled cluster methods. For the aromatic dimers at small separation, improved CCSD(T)–MP2 “high-level corrections” (HLCs) cause substantial reductions in the dissociation energy. For the bromine and iodine species, (n-1)d subvalence correlation increases dissociation energies, and turns out to be more important for noncovalent interactions than is generally realized. As in previous studies, we find that the most efficient way to obtain HLCs is to combine (T) from conventional CCSD(T) calculations with explicitly correlated CCSD-F12–MP2-F12 differences.</p>

scholarly journals Polyelectrolyte Gels Formed by Filamentous Biopolymers: Dependence of Crosslinking Efficiency on the Chemical Softness of Divalent Cations

Gels ◽  
2021 ◽  
Vol 7 (2) ◽  
pp. 41
Author(s):  
Katrina Cruz ◽  
Yu-Hsiu Wang ◽  
Shaina A. Oake ◽  
Paul A. Janmey
Keyword(s):  
Alkaline Earth ◽  
Divalent Cations ◽  
Transition Metal Ions ◽  
Atomic Weight ◽  
Mechanical Resistance ◽  
Flexible Polymers ◽  
Interpenetrating Networks ◽  
Charge Densities ◽  
Polyelectrolyte Gels ◽  
Different Types

Filamentous anionic polyelectrolytes are common in biological materials. Some examples are the cytoskeletal filaments that assemble into networks and bundled structures to give the cell mechanical resistance and that act as surfaces on which enzymes and other molecules can dock. Some viruses, especially bacteriophages are also long thin polyelectrolytes, and their bending stiffness is similar to those of the intermediate filament class of cytoskeletal polymers. These relatively stiff, thin, and long polyelectrolytes have charge densities similar to those of more flexible polyelectrolytes such as DNA, hyaluronic acid, and polyacrylates, and they can form interpenetrating networks and viscoelastic gels at volume fractions far below those at which more flexible polymers form hydrogels. In this report, we examine how different types of divalent and multivalent counterions interact with two biochemically different but physically similar filamentous polyelectrolytes: Pf1 virus and vimentin intermediate filaments (VIF). Different divalent cations aggregate both polyelectrolytes similarly, but transition metal ions are more efficient than alkaline earth ions and their efficiency increases with increasing atomic weight. Comparison of these two different types of polyelectrolyte filaments enables identification of general effects of counterions with polyelectrolytes and can identify cases where the interaction of the counterions and the filaments exhibits stronger and more specific interactions than those of counterion condensation.

scholarly journals Charge density studies on 1:1 co-crystals of ethenzamide and saccharin

2014 ◽  
Vol 70 (a1) ◽  
pp. C964-C964
Author(s):  
Lucy Mapp ◽  
Mateusz Pitak ◽  
Simon Coles ◽  
Srinivasulu Aitipamula
Keyword(s):  
Hydrogen Bonds ◽  
Charge Density ◽  
Crystal Engineering ◽  
Chemical Properties ◽  
Secondary Level ◽  
Crystal Form ◽  
Monoclinic Space Group ◽  
Stoichiometric Ratio ◽  
Distribution Analysis ◽  
Space Group

The study of multi-component crystals, as well as the phenomenon of polymorphism, both have relevance to crystal engineering. Obtaining a specific polymorph is crucial as different polymorphs usually exhibit different physical and chemical properties and often the origin of this behaviour is unknown. This is especially important in the pharmaceutical industry. Herein, we present results of comparative studies of an analgesic drug, ethenzamide and its co-crystals with saccharin. The co-crystalisation of ethenzamide (2-ethoxybenzamide, EA) with saccharin (1,1-dioxo-,1,2-benzothiazol-3-one, SAC) with a 1:1 stoichiometric ratio resulted in two polymorphic forms of the co-crystal. Form I crystallises in the triclinic P-1 space group, whereas form II crystallises in monoclinic space group P21/n. Previous crystal structure analyses on forms I and II revealed that in both polymorphs the primary carboxy-amide-imide heterosynthon is the same, however the secondary level of interactions which extends the hydrogen bond network is different. Form I consists of extended linear tapes via N-H···O hydrogen bonds, whereas form II is composed of stacks of tetrameric motifs including N-H···O hydrogen bonds and C-H···O interactions. These two forms of EA-SAC can be classified as synthon polymorphs at a secondary level of hydrogen bonding [1]. In our approach an accurate, high resolution charge density distribution analysis has been carried out to obtain greater insight into the electronic structures of both types of the EA-SAC co-crystals and relate differences in electronic distribution with their polymorphic behaviour. To describe the nature and role of inter and intra-molecular interactions in a quantitative manner, the Hansen-Coppens formalism [2] and Bader's AIM theory [3] approach have been applied.

Halogen Bonds in Crystal Engineering: Like Hydrogen Bonds yet Different

2014 ◽  
Vol 47 (8) ◽  
pp. 2514-2524 ◽  
Author(s):  
Arijit Mukherjee ◽  
Srinu Tothadi ◽  
Gautam R. Desiraju
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Halogen Bonds
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