Exploitation of the hydrogen bond: recent developments in the context of crystal engineering

Reversible Phase Transformations in a Double-Walled Diamondoid Coordination Network with a Stepped Isotherm for Methane

Flexible metal-organic materials (FMOMs) with stepped isotherms can offer enhanced working capacity in storage applications such as adsorbed natural gas (ANG) storage. Unfortunately, whereas >1000 FMOMs are known, only a handful exhibit methane uptake of >150 cm3/cm3 at 65 atm and 298 K, conditions relevant to ANG. Here, we report a double-walled 2-fold interpenetrated diamondoid (dia) network, X-dia-6-Ni, [Ni2L4(μ-H2O)]n, comprising a new azo linker ligand, L- (L- = (E)-3-(pyridin-4-yldiazenyl)benzoate) and 8-connected dinuclear molecular building blocks. X-dia-6-Ni exhibited gas (CO2, N2, CH4) and liquid (C8 hydrocarbons)-induced reversible transformations between its activated narrow-pore β phase and γ, a large-pore phase with ca. 33% increase in unit cell volume. Single-crystal X-ray diffraction (SCXRD) studies of the as-synthesized phase α, β, and γ revealed that structural transformations were enabled by twisting of the azo moiety and/or deformation of the MBB. Further insight into these transformations was gained from variable temperature powder XRD and in situ variable pressure powder XRD. Low-temperature N2 and CO2 sorption revealed stepped Type F-II isotherms with saturation uptakes of 422 and 401 cm3/g, respectively. X-dia-6-Ni exhibited uptake of 200 cm3/cm3 (65 atm, 298 K) and a high CH4 working capacity of 166 cm3/cm3 (5-65 bar, 298 K, 33 cycles), the third highest value yet reported for an FMOM and the highest value for an FMOM with a Type F-II isotherm.

EMMAs: Implementation and Assessment of a Suite of Cross-Disciplinary, Case-Based High School Activities to Explore Three-Dimensional Molecular Structure, Noncovalent Interactions, and Molecular Dynamics

Students frequently develop misconceptions about noncovalent interactions that make it challenging for them to appropriately interpret aspects of molecular structure and interactions critical to myriad applications. We hypothesized that computational molecular modeling and visualization could provide a valuable approach to help address these core misconceptions when students are first exposed to these concepts in secondary school chemistry courses. Here, we present a series of activities exploring biomolecular drug-target interactions using molecular visualization software and an introduction to molecular dynamics methods that were implemented in secondary school classrooms. A pre- and postsurvey approach that incorporated Likert response type, written free response, and drawing-based items demonstrated that students gained an enhanced conceptualization of intermolecular interactions, particularly related to aspects of shape complementarity, after completing the activities. Students also expressed increased comfort with and facility in utilizing different three-dimensional representations of molecules in their postsurvey responses. The activities led to an increased appreciation of interdisciplinary connections of chemistry with mathematics and physics. Overall, the modular activities presented provide a relatively time-efficient and accessible manner to help promote an understanding of a traditionally challenging topic for beginning chemistry students while introducing them to contemporary research tools.

Quasi-atomic orbital analysis of halogen bonding interactions

A quasi-atomic orbital analysis of the halogen bonded NH3⋯XF complexes (X = F, Cl, Br, and I) is performed to gain insight into the electronic properties associated with these σ-hole interactions. It is shown that significant sharing of electrons between the nitrogen lone pair of the ammonia molecule and the XF molecule occurs, resulting in a weakening of the X-F bond. In addition, the N-X bond shows increasing covalent character as the size of the halogen atom X increases. While the Mulliken outer complex NH3⋯XF appears to be overall the main species, the strength of the covalent interaction of the N-X bond becomes increasingly similar to that of the N-X bond in the [NH3X]+ cation as the size of X increases.

Supramolecular assemblies in the molecular complexes of 4-cyanophenylboronic acid with different N-donor ligands

Molecular complexes of 4-cyanophenylboronic acid (CB) with various N-donor compounds having different conformational features, for example, rigid (1,10-phenanthroline (110phen), 4,7-phenanthroline (47phen), 1,7-phenanthroline (17phen) and acridine (acr)) and linear (1,2-bis(4-pyridyl)ethane (bpyea), 1,2-bis(4-pyridyl)ethene (bpyee) and 4,4'-azopyridine (azopy)), have been reported. In all complexes, the -B(OH)2 moiety is found to be in a syn-anti confirmation, with the exception of structures containing 110phen, bpyee, and azopy, wherein, syn-syn conformation is observed. Further, CB molecules remain intact in all structures except in the complexes with some linear N-donor ligands, wherein -B(OH)2 transforms to monoester (-B(OH)(OCH3)) prior to the formation of corresponding molecular complexes. In such boronic monoester complexes, the conformation of -B(OH)(OCH3) is syn-anti with respect to the -OH and -OCH3 groups. Also, complexes mediated by azopy and bpyee exist in both hydrated and anhydrous forms. In these anhydrous structures, the recognition pattern is through homomeric (juxtaposed -CN and -B(OH)2) as well as heteromeric (between hetero N-atom and -B(OH)2) O-H⋯N hydrogen bonds, while only heteromeric O-H⋯N hydrogen bonds hold co-formers in all other structures. Depending upon the conformational features of both co-formers, molecules are packed in crystal lattices in the form of stacked layers, helical chains, and crossed ribbons. All structures are fully characterized by single-crystal X-ray diffraction and phase purity is established by powder X-ray diffraction. Additionally, correlation among structures is explained by calculating a similarity index and performing a Hirshfeld surface analysis to quantify the strength and effectiveness of different types of intermolecular bonds that stabilize these structures along with the presentation of energy frameworks, representing the strength of the interactions in the form gradient cylinders. Also, the morphology of each complex was computed by BFDH methodology to correlate with the actual crystal morphology and packing arrangement.

Dative B←N bonds based crystalline organic framework with permanent porosity for acetylene storage and separation

The utilization of dative B←N bonds for the creation of crystalline organic framework (BNOF) has increasingly received intensive interest; however, the shortage of permanent porosity is an obstacle that must be overcome to guarantee their application as porous materials. Here, we report the first microporous crystalline framework, BNOF-1, that is assembled through sole monomers, which can be scalably synthesized by the cheap 4-pyridine boronic acid. The 2D networks of BNOF-1 were stacked in parallel to generate a highly porous supramolecular open framework, which possessed not only the highest BET surface area of 1345 m² g^-1 amongst all of the BNOFs but also features a record-high uptake of C₂H₂ and CO₂ in covalent organic framework (COF) materials to date. Dynamic breakthrough experiments demonstrated that BNOF-1 material can efficiently separate C₂H₂/CO₂ mixtures. In addition, the network can be regenerated in organic solvents with no loss in performance, making its solution processable. We believe that BNOF-1 would greatly diversify the reticular chemistry and open new avenues for the application of BNOFs.

Expanding the Scope of Metastable Species in Hydrogen Bonding-Directed Supramolecular Polymerization

We reveal unique hydrogen (H-) bonding patterns and exploit them to control the kinetics, pathways and length of supramolecular polymers (SPs). New bisamide-containing monomers were designed to elucidate the role of competing intra- vs. intermolecular H-bonding interactions on the kinetics of supramolecular polymerization (SP). Remarkably, two polymerization-inactive metastable states were discovered. Contrary to previous examples, the commonly assumed intramolecularly H-bonded monomer does not evolve into intermolecularly H-bonded SPs via ring opening, but rather forms a metastable dimer. In this dimer, all H-bonding sites are saturated, either intra- or intermolecularly, hampering elongation. The dimers exhibit an advantageous preorganization, which upon opening of the intramolecular portion of the H-bonding motif facilitates SP in a consecutive process. The retardation of spontaneous self-assembly as a result of two metastable states enables length control in SP by seed-mediated growth.

Supramolecular polymerization of thiobarbituric acid naphthalene dye

2-Thiobarbituric acid-functionalized naphthalene dye selectively self-assembles into crystalline fibers to show material properties that are different from those of a previously reported oxo-barbituric acid derivative affording curved supramolecular polymers via...

Inorganic Salts of N-phenylbiguanidium(1+)-Novel Family with Promising Representatives for Nonlinear Optics

Seven inorganic salts containing N-phenylbiguanide as a prospective organic molecular carrier of nonlinear optical properties were prepared and studied within our research of novel hydrogen-bonded materials for nonlinear optics (NLO). All seven salts, namely N-phenylbiguanidium(1+) nitrate (C2/c), N-phenylbiguanidium(1+) perchlorate (P-1), N-phenylbiguanidium(1+) hydrogen carbonate (P21/c), bis(N-phenylbiguanidium(1+)) sulfate (C2), bis(N-phenylbiguanidium(1+)) hydrogen phosphate sesquihydrate (P-1), bis(N-phenylbiguanidium(1+)) phosphite (P21), and bis(N-phenylbiguanidium(1+)) phosphite dihydrate (P21/n), were characterised by X-ray diffraction (powder and single-crystal X-ray diffraction) and by vibrational spectroscopy (FTIR and Raman). Two salts with non-centrosymmetric crystal structures-bis(N-phenylbiguanidium(1+)) sulfate and bis(N-phenylbiguanidium(1+)) phosphite-were further studied to examine their linear and nonlinear optical properties using experimental and computational methods. As a highly SHG-efficient and phase-matchable material transparent down to 320 nm and thermally stable to 483 K, bis(N-phenylbiguanidium(1+)) sulfate is a promising novel candidate for NLO.

Two Faces of Water in the Formation and Stabilization of Multicomponent Crystals of Zwitterionic Drug-Like Compounds

Two new hydrated multicomponent crystals of zwitterionic 2-aminonicotinic acid with maleic and fumaric acids have been obtained and thoroughly characterized by a variety of experimental (X-ray analysis and terahertz Raman spectroscopy) and theoretical periodic density functional theory calculations, followed by Bader analysis of the crystalline electron density) techniques. It has been found that the Raman-active band in the region of 300 cm−1 is due to the vibrations of the intramolecular O-H...O bond in the maleate anion. The energy/enthalpy of the intermolecular hydrogen bonds was estimated by several empirical approaches. An analysis of the interaction networks reflects the structure-directing role of the water molecule in the examined multicomponent crystals. A general scheme has been proposed to explain the proton transfer between the components during the formation of multicomponent crystals in water. Water molecules were found to play the key role in this process, forming a “water wire” between the COOH group of the dicarboxylic acid and the COO– group of the zwitterion and the rendering crystal lattice of the considered multicomponent crystals.

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

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.

Self-assembly and photocatalytic property of a new inorganic-organic hybrid material based on 1,4-bis(4-pyridylthio)butane

A new hybrid compound consisting of 1,4-bis(4-pyridylthio)butane ([Bpytb]) ligand, namely {[Bpytb]Ag2I3}n (1), has been prepared and characterized by IR spectroscopy, solid UV-visible diffuse reflectance spectrum, X-ray Powder Diffraction (PXRD) and TG. Compound 1 consists of 1D anion chain structure. Crystal system: Monoclinic, Space group: P2/c, a = 4.5092(3), b = 11.1895(9), c = 21.3893(14), α= 90°, β= 92.907(2)°, γ= 90°, V = 1077.82(13) Å3, Z = 2, Dcalc = 2.693 g cm–3. The photocatalytic property of compound 1 was also studied and it exhibits a better degradation effect on organic dye MB.

A Co8 metallacycle stabilized by double anion–π interactions

The syntheses, crystal structures and magnetic studies of two new Co^II 2,2′-bipyrimidine bridged complexes stabilized by hydrogen bonding versus anion–π interactions are reported.

Encapsulation of a Water Octamer Chain in a Chiral 2D Sheetlike Supramolecular Coordination Network Composed of Dinickel-Dicarboxylate Subunits

Four new chiral supramolecular coordination networks of Ni(II) of general formula [Ni₂(Hhissal)₂(dicarboxylate)(H₂O)₂]·nH₂O (where Hhissal = histidinesalicylate; dicarboxylate = adipate; n = 8 for 1, succinate; n = 4 for 2, maleate; n = 4 for 3, fumarate; and n = 6 for 4) are reported. On the basis of the single-crystal X-ray study, an unprecedented zig-zag chain structure of water octamer encapsulated in 1 has been identified. The supramolecular network of the dimetal subunits is formed through hydrogen bonding interactions between the amine N-H of Hhissal and the oxygen atom of the coordinated water molecule of one subunit with the uncoordinated oxygen atom and the coordinated oxygen atom of the carboxylate group of Hhissal of the next subunit, respectively. The strength of hydrogen bonding within this water cluster (the range of O···O distances is 2.702-2.760 Å) is similar to that found in ice. These networks are further characterized by elemental analysis, IR spectroscopy, powder X-ray diffraction, polarimetry, UV-vis/diffuse reflectance and circular dichroism spectroscopy, and thermogravimetric analysis. A comparison of their properties indicates that these are isostructural with a variation of encapsulated water clusters.

Chirality at two-dimensional surfaces: A perspective from small molecule alcohol assembly on Au(111)

The delicate balance between hydrogen bonding and van der Waals interactions determines the stability, structure, and chirality of many molecular and supramolecular aggregates weakly adsorbed on solid surfaces. Yet the inherent complexity of these systems makes their experimental study at the molecular level very challenging. In this quest, small alcohols adsorbed on metal surfaces have become a useful model system to gain fundamental insight into the interplay of such molecule-surface and molecule-molecule interactions. Here, through a combination of scanning tunneling microscopy and density functional theory, we compare and contrast the adsorption and self-assembly of a range of small alcohols from methanol to butanol on Au(111). We find that longer chained alcohols prefer to form zigzag chains held together by extended hydrogen bonded networks between adjacent molecules. When alcohols bind to a metal surface datively via one of the two lone electron pairs of the oxygen atom, they become chiral. Therefore, the chain structures are formed by a hydrogen-bonded network between adjacent molecules with alternating adsorbed chirality. These chain structures accommodate longer alkyl tails through larger unit cells, while the position of the hydroxyl group within the alcohol molecule can produce denser unit cells that maximize intermolecular interactions. Interestingly, when intrinsic chirality is introduced into the molecule as in the case of 2-butanol, the assembly changes completely and square packing structures with chiral pockets are observed. This is rationalized by the fact that the intrinsic chirality of the molecule directs the chirality of the adsorbed hydroxyl group meaning that heterochiral chain structures cannot form. Overall this study provides a general framework for understanding the effect of simple alcohol molecular adstructures on hydrogen bonded aggregates and paves the way for rationalizing 2D chiral supramolecular assembly.

The role of different nonspecific interactions and halogen contacts in the crystal structure organization of 5-chloroisatoic anhydride

The crystal structure of 6-chloro-2,4-dihydro-1H-3,1-benzoxazine-2,4-dione (5-chloroisatoic anhydride), C₈H₄ClNO₃, has been determined and analysed in terms of connectivity and packing patterns. The compound crystallizes in the noncentrosymmetric space group Pna2₁ with one molecule in the asymmetric unit. The role of different weak interactions is discussed with respect to three-dimensional network organization. Molecules are extended into one-dimensional helical arrangements, making use of N-H...O hydrogen bonds and π-π interactions. The helices are further organized into monolayers via weak C-H...O and lone pair-π interactions, and the monolayers are packed into a noncentrosymmetric three-dimensional architecture by C-Cl...π interactions and C-H...Cl and Cl...Cl contacts. A Hirshfeld surface (HS) analysis was carried out and two-dimensional (2D) fingerprint plots were generated to visualize the intermolecular interactions and to provide quantitative data for their relative contributions. In addition, tests of the antimicrobial activity and in vitro cytotoxity effects against fitoblast L929 were performed and are discussed.

Enhancement of microphase ordering and mechanical properties of supramolecular hydrogen-bonded polyurethane networks

Enhanced thermoreversible and mechanical properties in supramolecular polyurethanes have been realised by the incorporation of flexible DBDI derived hard segments.

Structural phase diagrams and isomerism inflexible honeycomb-like 2D hydrogen bonded solid solutions

Solid solutions of hydrogen bonded networks of the formula ((1-2H⁺)_3x(2-2H⁺)_3(1–x)([Fe(CN)₆]₂³⁻))·nH₂O, where (1-2H⁺) and (2-2H⁺) are bisamidinium H bond donor entities, have been prepared and structurally analysed.

Distribution of valence electrons of the flavin cofactor in NADH-cytochrome b5 reductase

Flavin compounds such as flavin adenine dinucleotide (FAD), flavin mononucleotide and riboflavin make up the active centers in flavoproteins that facilitate various oxidoreductive processes. The fine structural features of the hydrogens and valence electrons of the flavin molecules in the protein environment are critical to the functions of the flavoproteins. However, information on these features cannot be obtained from conventional protein X-ray analyses at ordinary resolution. Here we report the charge density analysis of a flavoenzyme, NADH-cytochrome b₅ reductase (b5R), at an ultra-high resolution of 0.78 Å. Valence electrons on the FAD cofactor as well as the peptide portion, which are clearly visualized even after the conventional refinement, are analyzed by the multipolar atomic model refinement. The topological analysis for the determined electron density reveals the valence electronic structure of the isoalloxazine ring of FAD and hydrogen-bonding interactions with the protein environment. The tetrahedral electronic distribution around the N5 atom of FAD in b5R is stabilized by hydrogen bonding with C_αH of Tyr65 and amide-H of Thr66. The hydrogen bonding network leads to His49 composing the cytochrome b₅-binding site via non-classical hydrogen bonds between N5 of FAD and C_αH of Tyr65 and O of Tyr65 and C_βH of His49.

Crystal structure of 1,2-bis-[(1H-imidazol-2-yl)methylidene]hydrazine and its one-dimensional hydrogen-bonding network

In the title compound, C8H8N6, two imidazolyl groups are separated by a zigzag -CH=N-N=CH- linkage. An inversion center is located at the mid-point of the N-N single bond and the complete molecule is generated by symmetry. In the crystal, each mol-ecule forms four N-H⋯N hydrogen bonds with two neighbouring mol-ecules to constitute a one-dimensional ladder-like structure propagating along the a-axis direction.

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

Ancillary ligand assisted self-assembly of coordination architectures of Mn(ii): the effect of the N-alkyl group on a tridentate ligand

For the first time it is shown that a subtle change in the N-alkyl group (methyl or ethyl) of a tridentate ancillary ligand, bis(2-pyridylmethyl)alkylamine, is responsible for the diversity of product formation under similar conditions. Through their water vapor adsorption study, a structure-property correlation is established.

Controlling the self-assembly of homochiral coordination architectures of CuII by substitution in amino acid based ligands: synthesis, crystal structures and physicochemical properties

In this paper we report six chiral ligands based on l-tyrosine, l-serine and l-phenylalanine and their homochiral Cu^II complexes to study the effect of various substitutions in the ligands on the formation of diverse coordination architectures.

Construction of POMOFs with different degrees of interpenetration and the same topology

Three POMOFs with different degrees of interpenetration are reported and the influence of the organic molecules on the degree of interpenetration of the compounds is discussed.

Hierarchical importance of coordination and hydrogen bonds in the formation of homochiral 2D coordination polymers and 2D supramolecular assemblies

2D homochiral coordination polymers and their conversion to the corresponding homochiral 2D supramolecular assemblies using 4,4’-bipyridine as a bifunctional linker are reported.