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Influence of donor point modifications on the assembly of chalcogen-bonded organic frameworks
Abstract
Systematic replacement of selenium for tellurium in a chalcogen-bonding tecton results in divergent assembly behavior from competitive solvents.
Mesoporous molecular crystals have potential applications in separation and catalysis, but they are rare and hard to design because many weak interactions compete during crystallization, and most molecules have an energetic preference for close packing. Here, we combine crystal structure prediction (CSP) with structural invariants to continuously qualify the similarity between predicted crystal structures for related molecules. This allows isomorphous substitution strategies, which can be unreliable for molecular crystals, to be augmented by a priori prediction, thus leveraging the power of both approaches. We used this combined approach to discover a rare example of a low-density (0.54 g cm-3) mesoporous hydrogen-bonded framework (HOF), 3D-CageHOF-1. This structure comprises an organic cage (Cage-3-NH2) that was predicted to form kinetically trapped, low-density polymorphs via CSP. Pointwise distance distribution structural invariants revealed five predicted forms of Cage-3-NH2 that are analogous to experimentally realized porous crystals of a chemically different but geometrically similar molecule, T2. More broadly, this approach overcomes the difficulties in comparing predicted molecular crystals with varying lattice parameters, thus allowing for the systematic comparison of energy-structure landscapes for chemically dissimilar molecules.
This recommendation proposes a definition for the term “chalcogen bond”; it is recommended the term is used to designate the specific subset of inter- and intramolecular interactions formed by chalcogen atoms wherein the Group 16 element is the electrophilic site.
Designing organic components that can be used to construct porous materials enables the preparation of tailored functionalized materials. Research into porous materials has seen a resurgence in the past decade as a result of finding of self‐standing porous molecular crystals (PMCs). Particularly, a number of crystalline systems with permanent porosity that are formed by self‐assembly through hydrogen bonding (H‐bonding) have been developed. Such systems are called hydrogen‐bonded organic frameworks (HOFs). Herein we systematically describe H‐bonding patterns (supramolecular synthons) and molecular structures (tectons) that have been used to achieve thermal and chemical durability, a large surface area, and functions, such as selective gas sorption and separation, which can provide design principles for constructing HOFs with permanent porosity.
The secondary building unit (SBU) approach was a turning point in the discovery of permanently porous metal-organic frameworks (MOFs) and in launching the field of reticular chemistry. In contrast to the single-metal nodes known in coordination networks, the polynuclear nature of SBUs allows these structures to serve as rigid, directional, and stable building units in the design of robust crystalline materials with predetermined structures and properties. This concept has also enabled the development of MOFs with ultra-high porosity and structural complexity. The architectural, mechanical, and chemical stability of MOFs imparted by their SBUs also gives rise to unique framework chemistry. All of this chemistry –including ligand, linker, metal exchange, and metallation reactions, as well as precisely controlled formation of ordered vacancies– is carried out with full retention of the MOF structure, crystallinity, and porosity. The unique chemical nature of SBUs makes MOFs useful in many applications including gas and vapor adsorption, separation processes, and SBU-mediated catalysis. In essence, the SBU approach realizes a long-standing dream of scientists by bringing molecular chemistry (both organic and inorganic) to extended solid-state structures. This contribution highlights the importance of the SBUs in the development of MOFs and points to the tremendous potential still to be harnessed.
In the last few decades, “unusual” noncovalent interactions like anion‐π and halogen bonding have emerged as interesting alternatives to the ubiquitous hydrogen bonding in many research areas. This is also true, to a somewhat lesser extent, for chalcogen bonding, the noncovalent interaction involving Lewis acidic chalcogen centers. Herein, we aim to provide an overview on the use of chalcogen bonding in crystal engineering and in solution, with a focus on the recent developments concerning intermolecular chalcogen bonding in solution‐phase applications. In the solid phase, chalcogen bonding has been used for the construction of nano‐sized structures and the self‐assembly of sophisticated self‐complementary arrays. In solution, until very recently applications mostly focused on intramolecular interactions which stabilized the conformation of intermediates or reagents. In the last few years, intermolecular chalcogen bonding has increasingly also been exploited in solution, most notably in anion recognition and transport as well as in organic synthesis and organocatalysis.
N-Methyl-2-Pyrrolidone (NMP) is an exceptional solvent, widely used in industry and for nanomaterials processing. Yet despite its ubiquity, its liquid structure, which ultimately dictates its solvent properties, is not fully known. Here, neutron scattering is used to determine NMP's structure in unprecedented detail. Two dominant nearest-neighbor arrangements are found, where rings are parallel or perpendicular. However, compared with related solvents, NMP has a relatively large population of parallel approaches, similar only to benzene, despite its non-aromaticity and the presence of the normally structure-reducing methyl group. This arrangement is underpinned by NMP's dipole moment, which has a profound effect on its structure: nearest-neighbor molecules arrange in an anti-parallel but offset fashion. This polar-induced order extends beyond the first solvation shell, resulting in ordered trimers that reach the nanometer range. The degree of order and balance of interactions rationalize NMP's high boiling point and versatile capabilities to solvate charged and uncharged species.
Chalcogen bonding is a type of noncovalent interaction in which a covalently bonded chalcogen atom (O, S, Se or Te) acts as an electrophilic species towards a nucleophilic (negative) region(s) in another or in the same molecule. In general, this interaction is strengthened by the presence of an electron-withdrawing group on the electron-acceptor chalcogen atom and upon moving down in the periodic table of elements, from O to Te. Following a short discussion of the phenomenon of chalcogen bonding, this Perspective presents some demonstrative experimental observations in which this bonding is crucial for synthetic transformations, crystal engineering, catalysis and design of materials as synthons/tectons.
Organic molecules with heavy main-group elements frequently form supramolecular links to electron-rich centres. One particular case of such interactions is halogen bonding. Most studies of this phenomenon have been concerned with either dimers or infinitely extended structures (polymers and lattices) but well-defined cyclic structures remain elusive. Here we present oligomeric aggregates of heterocycles that are linked by chalcogen-centered interactions and behave as genuine macrocyclic species. The molecules of 3-methyl-5-phenyl-1,2-tellurazole 2-oxide assemble a variety of supramolecular aggregates that includes cyclic tetramers and hexamers, as well as a helical polymer. In all these aggregates, the building blocks are connected by Te ⋯ O-N bridges. Nuclear magnetic resonance spectroscopic experiments demonstrate that the two types of annular aggregates are persistent in solution. These self-assembled structures form coordination complexes with transition-metal ions, act as fullerene receptors and host small molecules in a crystal.
The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.
Metal-organic and covalent organic frameworks are porous materials characterized by outstanding thermal stability, high porosities and modular synthesis. Their repeating structures offer a great degree of control over pore sizes, dimensions and surface properties. Similarly precise engineering at the nanoscale is difficult to achieve with discrete molecules, since they rarely crystallize as porous structures. Here we report a small organic molecule that organizes into a noncovalent organic framework with large empty pores. This structure is held together by a combination of [N-H···N] hydrogen bonds between the terminal pyrazole rings and [π···π] stacking between the electron-rich pyrazoles and electron-poor tetrafluorobenzenes. Such a synergistic arrangement makes this structure stable to at least 250 °C and porous, with an accessible surface area of 1,159 m(2) g(-1). Crystals of this framework adsorb hydrocarbons, CFCs and fluorocarbons-the latter two being ozone-depleting substances and potent greenhouse species-with weight capacities of up to 75%.
The equilibrium structures, binding energies, vibrational harmonic frequencies, and the anharmonic corrections for two different
(cyclic and asymmetric) urea dimers and for the adenine–thymine DNA base pair system have been studied using the second-order
Møller–Plesset perturbation theory (MP2) method and different density functional theory (DFT) exchange–correlation (XC) functionals
(BLYP, B3LYP, PBE, HCTH407, KMLYP, and BH and HLYP) with the D95V, D95V**, and D95V++** basis sets. The widely used a posteriori
Boys–Bernardi or counterpoise correction scheme for basis set superposition error (BSSE) has been included in the calculations
to take into account the BSSE effects during geometry optimization (on structure), on binding energies and on the different
levels of approximation used for calculating the vibrational frequencies. The results obtained with the ab initio MP2 method
are compared with those calculated with different DFT XC functionals; and finally the suitability of these DFT XC functionals
to describe intermolecular hydrogen bonds as well as harmonic frequencies and the anharmonic corrections is assessed and discussed.
Fully exploiting the properties of graphene will require a method for the mass production of this remarkable material. Two main routes are possible: large-scale growth or large-scale exfoliation. Here, we demonstrate graphene dispersions with concentrations up to approximately 0.01 mg ml(-1), produced by dispersion and exfoliation of graphite in organic solvents such as N-methyl-pyrrolidone. This is possible because the energy required to exfoliate graphene is balanced by the solvent-graphene interaction for solvents whose surface energies match that of graphene. We confirm the presence of individual graphene sheets by Raman spectroscopy, transmission electron microscopy and electron diffraction. Our method results in a monolayer yield of approximately 1 wt%, which could potentially be improved to 7-12 wt% with further processing. The absence of defects or oxides is confirmed by X-ray photoelectron, infrared and Raman spectroscopies. We are able to produce semi-transparent conducting films and conducting composites. Solution processing of graphene opens up a range of potential large-area applications, from device and sensor fabrication to liquid-phase chemistry.
We developed a series of single atom catalysts (SACs) anchored on bipyridine-rich COFs. By tuning the active metal center, the optimal Py-Bpy-COF-Zn shows the highest selectivity of 99.1% and excellent...
The first polyoxometalate-encapsulated twenty-four-nucleus organophosphorus-copper nanocage cluster organic framework has been constructed and it is shown to exhibit highly efficient bifunctional electrochemical performance.
We examined the dielectric (DE) and nuclear magnetic resonance (NMR) spectroscopic behaviour of N-methyl-2-pyrroridone (NMP) and N,N-dimethylacetamide (DMAc), which are tertiary amide compounds that bear five-membered cyclic and open structures,...
Hydrogen-bonded organic framework (HOF)-based catalysts still remain unreported thus far due to their relatively weak stability. In the present work, a robust porous HOF (HOF-19) with a Brunauer-Emmett-Teller surface area of 685 m2 g‒1 was reticu-lated from a cage-like building block, amino-substituted bis(tetraoxacalix[2]arene[2]triazine), depending on the hydro-gen bonding with the help of - interactions. The post-synthetic metalation of HOF-19 with palladium acetate afforded a palladium(II)-containing heterogeneous catalyst with hydro-gen-bonded structure retained, which exhibits excellent catalyt-ic performance for Suzuki-Miyaura coupling reaction with the high isolation yields (96~98%), prominent stability, and good selectivity. More importantly, by simple recrystallization, the catalytic activity of deactivated species can be recovered from the isolation yield 46% to 92% for 4-bromobenzonitrile conver-sion at the same conditions, revealing the great application potentials of HOF-based catalysts.
The distribution of the electron density around covalently bonded atoms is anisotropic, and this determines the presence, on atoms surface, of areas of higher and lower electron density where the electrostatic potential is frequently negative and positive, respectively. The ability of positive areas on atoms to form attractive interactions with electron rich sites became recently the subject of a flurry of papers. The halogen bond (HaB), the attractive interaction formed by halogens with nucleophiles, emerged as a quite common and dependable tool for controlling phenomena as diverse as the binding of small molecules to proteinaceous targets or the organization of molecular functional materials. The mindset developed in relation to the halogen bond prompted the interest in the tendency of elements of groups 13-16 of the periodic table to form analogous attractive interactions with nucleophiles. This Account addresses the chalcogen bond (ChB), the attractive interaction formed by group 16 elements with nucleophiles, by adopting a crystallographic point of view. Structures of organic derivatives are considered where chalcogen atoms form close contacts with nucleophiles in the geometry typical for chalcogen bonds. It is shown how sulfur, selenium, and tellurium can all form chalcogen bonds, the tendency to give rise to close contacts with nucleophiles increasing with the polarizability of the element. Also oxygen, when conveniently substituted, can form ChBs in crystalline solids. Chalcogen bonds can be strong enough to allow for the interaction to function as an effective and robust tool in crystal engineering. It is presented how chalcogen containing heteroaromatics, sulfides, disulfides, and selenium and tellurium analogues as well as some other molecular moieties can afford dependable chalcogen bond based supramolecular synthons. Particular attention is given to chalcogen containing azoles and their derivatives due to the relevance of these moieties in biosystems and molecular materials. It is shown how the interaction pattern around electrophilic chalcogen atoms frequently recalls the pattern around analogous halogen, pnictogen, and tetrel derivatives. For instance, directionalities of chalcogen bonds around sulfur and selenium in some thiazolium and selenazolium derivatives are similar to directionalities of halogen bonds around bromine and iodine in bromonium and iodonium compounds. This gives experimental evidence that similarities in the anisotropic distribution of the electron density in covalently bonded atoms translates in similarities in their recognition and self-assembly behavior. For instance, the analogies in interaction patterns of carbonitrile substituted elements of groups 17, 16, 15, and 14 will be presented. While the extensive experimental and theoretical data available in the literature prove that HaB and ChB form twin supramolecular synthons in the solid, more experimental information has to become available before such a statement can be safely extended to interactions wherein elements of groups 14 and 15 are the electrophiles. It will nevertheless be possible to develop some general heuristic principles for crystal engineering. Being based on the groups of the periodic table, these principles offer the advantage of being systematic.
The recent progress in the synthesis of the title heterocycles exemplified by closed‐ and open‐shell 1,2,5‐chalcogenadiazoles, 1,2,3‐dichalcogenazoles and their hybrids (chalcogens: S, Se, and Te), and in actual or potential applications of these compounds in materials science and biomedicine, are discussed. Synthetic importance of the chalcogen exchange, both direct and indirect, is emphasized, as well as significance of the heavier chalcogen derivatives in the design and synthesis of smart molecular materials.
Hydrogen-bonded organic frameworks (HOFs), a new type of porous material following the metal-organic frameworks (MOFs), covalent organic frameworks (COFs), etc., have emerged as one of the promising candidates in diverse...
Derivatives of 2,1,3-benzothiadiazole (1) are widely used in many areas of science and are particularly valuable as components of active layers in various thin-film optoelectronic devices. Even more effective benzothiadiazoles are likely to result if a deeper understanding of their preferred patterns of molecular association can be acquired. To provide new insight, we have analyzed the structures of compounds in which multiple benzothiadiazole units are attached to well-defined planar and nonplanar molecular cores. Our results show that molecular organization can be controlled in complex structures by using directional S...N bonding of benzothiadiazole units and other characteristic interactions. Moreover, the observed structures are distinctly different from those of analogous arenes. Replacing benzene rings in arenes by thiadiazoles thereby provides a strategy for making new compounds with extended systems of pi-conjugation and unique patterns of molecular organization, including the ability to co-crystallize with the fullerenes C60 and C70.
A framework for molecular assembly
Covalent molecular frameworks are crystalline microporous materials assembled from organic molecules through strong covalent bonds in a process termed reticular synthesis. Diercks and Yaghi review developments in this area, noting the parallels between framework assembly and the covalent assembly of atoms into molecules, as described just over a century ago by Lewis. Emerging challenges include functionalization of existing frameworks and the creation of flexible materials through the design of woven structures.
Science , this issue p. eaal1585
A hydrogen-bonded organic framework (HOF) was constructed by avoiding potential π-π stacking of building blocks with robust and non-coplanar triptycene-based modules. The tailored-fitting interactions were demonstrated by the adsorption of fullerene with a concentration enrichment of ∼420 times in the pores.
Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal–organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy–structure–function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy–structure–function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.
Small molecule, large surface area: A rigid triptycene derivative self-assembles by hydrogen bonds to a porous crystal with one-dimensional channels of about 14 Å diameter. Solvents in the channels can be removed to generate an extrinsic porous material with a specific BET surface area of 2796 m2 g−1. Furthermore, gases can be selectively adsorbed within the pores at 1 bar.
Porous solids are important as membranes, adsorbents, catalysts, and in other chemical applications. But for these materials to find greater use at an industrial scale, it is necessary to optimize multiple functions in addition to pore structure and surface area, such as stability, sorption kinetics, processability, mechanical properties, and thermal properties. Several different classes of porous solids exist, and there is no one-size-fits-all solution; it can therefore be challenging to choose the right type of porous material for a given job. Computational prediction of structure and properties has growing potential to complement experiment to identify the best porous materials for specific applications.
Copyright © 2015, American Association for the Advancement of Science.
An unusual even-numbered bromination of triptycene tristhiadiazole is described, giving selectively dibromo-, tetrabromo-, and hexabromotriptycenes with two bromines each at the same phenyl ring. The new compounds can be used as precursors for extended π-conjugated systems and polymers.
We present a density functional theory [M06-2X/6-31+G(d,p)] study of the structures and free energies of formation of oligomers of four carboxylic acids (formic acid, acetic acid, tetrolic acid and benzoic acid) in water, chloroform and carbon tetrachloride. Solvation effects were treated using the SMD continuum solvation model. The low-lying energy structures of molecular complexes were located by adopting an efficient search procedure to probe the potential energy surfaces of the oligomers of carboxylic acids (CA)n (n = 2-6) The free energies of the isomers of (CA)n in solution were determined as the sum of the electronic energy, vibrational-rotational-translational gas-phase contribution and solvation free energy. The assessment of the computational protocol adopted in this study with respect to the dimerization of acetic acid, (AA)2, and formic acid, (FA)2, locates new isomers of (AA)2 and (FA)2 and gave dimerization constants in good agreement with the experimental values. The calculation of the self-association of acetic acid, tetrolic acid and benzoic acid shows the following: (i) Classic carboxylic dimers are the most stable isomer of (CA)2 in both the gas phase and solution; (ii) Trimers of carboxylic acid are stable in apolar aprotic solvents; (iii) Molecular clusters consisting of two interacting classic carboxylic dimers (D+D)T are the most stable type of tetramers but their formation from the self-association of classic carboxylic dimers is highly unfavourable; (iv) For acetic acid and tetrolic acid the reactions (CA)2 + 2CA → (D+D)T and (CA)3 + CA → (D+D)T are exoergonic but these aggregation pathways go through unstable clusters that could hinder the formation of tetrameric species; (v) For tetrolic acid the pre-nucleation species that are more likely to form in solution are dimeric and trimeric structures that have encoded structural motifs resembling the α- and β-solid forms of tetrolic acid; (vi) Stable tetramers of benzoic acid could form in carbon tetrachloride from the aggregation of trimers and monomers; (vii) Higher order clusters such as acetic acid pentamers and tetrolic acid hexamers are highly unstable in all solvation environments.
This paper presents experimental results obtained in the extraction of aromatic hydrocarbons with mixed N-methylpyrrolidone/glycol solvent from a 105-140 degree C cut of catalytic reformate. To determine the optimal N-methylpyrrolidone/glycol ratio, the authors first conducted experiments on the extraction of aromatic hydrocarbons from artificial blends with nonaromatic hydrocarbons. The experiments consisted of single-stage extractions in a thermostated separating funnel at 50 degree C with a 2:1 weight ratio of solvent to feedstock. From the results of these experiments, they calculated the distribution coefficients of the aromatic hydrocarbons K//a, the degree of their recovery, and the solvent/feedstock ratio required for complete recovery of the aromatics. Experimental data are tabulated and discussed. Experiments on the extraction of aromatic hydrocarbons from a 105-140 degree C cut of catalytic reformate in a countercurrent column confirmed the high efficiency of this mixed solvent; with a 3:1 weight ratio of solvent to feedstock and a temperature of 50 degree C, the recovery of xylenes and ethylbenzene was 99%. The content of aromatic hydrocarbons in the extract approached 100%.
The solubility of anthracene in N,N-dimethyformamide, N,N-dimethylacetamide, and N-methyl-2-pyrrolidone was determined respectively at temperatures ranging from (293.25 to 358.45) K, (293.15 to 359.25) K, and (293.45 to 357.55) K at atmosphere pressure. The experimental solubility was correlated by the equation ln x = A + B/T + C ln T.
The long-standing challenge of designing and constructing new crystalline solid-state materials from molecular building blocks is just beginning to be addressed with success. A conceptual approach that requires the use of secondary building units to direct the assembly of ordered frameworks epitomizes this process: we call this approach reticular synthesis. This chemistry has yielded materials designed to have predetermined structures, compositions and properties. In particular, highly porous frameworks held together by strong metal–oxygen–carbon bonds and with exceptionally large surface area and capacity for gas storage have been prepared and their pore metrics systematically varied and functionalized.
1,2,5-Chalcogenadiazoles, in particular the tellurium derivatives, are promising building blocks for the assembly supramolecular structures through the formation of the [E–N]2 (E = S, Se, Te) supramolecular synthon. This short account summarizes initial experimental and computational investigations in this area.
The crystal structures of tellurium compounds frequently display intermolecular contacts between the chalcogen and atoms possessing lone pairs of electrons. Analysis of the data deposited in the Cambridge crystallographic database shows that the shortest secondary bonding interactions (SBIs) are formed when oxygen, nitrogen or chlorine are the donor atoms for SBIs. In addition, these SBIs are shortest when they occur opposite to a bond between tellurium and oxygen, nitrogen, fluorine, chlorine or the nitrile functional group. The structural motifs assembled in these systems fall within eight general categories, from single to multiple bonded supramolecular synthons. The use of multiple points of attachment between molecules leads, in principle, to stronger and more directional supramolecular synthons. The overall structures assembled by the most important tellurium-based supramolecular synthons and prospects for their application in crystal engineering are discussed.
A large number of theoretical methods, ranging from classical calculations to high-level ab initio computations, have been used to study the dimerization of formic and acetic acids in the gas phase. Analysis of the results allows us to determine the range of accuracy expected for the different theoretical methods in the study of these types of interactions. The reasons for the errors occurring at high-level ab initio theory are discussed. Finally, the effect of the solvent on the dimerization of carboxylic acids is introduced using QM-SCRF, and MC-FEP methods. The reliability of both types of calculations is discussed. Results show that polar solvents play a key role in modulating the energetics of the dimerization of carboxylic acids. Dimerization free energies in the gas phase (1 atm) are found to be around −2 to −4 kcal/mol, values which are similar to those obtained in (1 M) chloroform solution. Dimerization free energies in (1 M) water are clearly positive (around 4−5 kcal/mol).
The study of porosity in the context of crystal engineering is rapidly growing in intensity. However, claims of porosity are often highly subjective and use of the term "porous" is susceptible to abuse. This contribution discusses some of the criteria to be considered when stating that a particular crystal structure is porous.
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