Inclusion Of Solvent Molecules Research Articles

One-step Access to Resorcinsalens-Solvent-Dependent Synthesis, Tautomerism, Self-sorting and Supramolecular Architectures of Chiral Polyimine Analogues of Resorcinarene.

Substituted 2,4- and 4,6-dihydroxyisophthalaldehydes were condensed with optically pure and racemic trans-1,2-diaminocyclohexane to form resorcinarene-like polyimine macrocycles (resorcinsalens), the structure and stoichiometry of which were controlled by the choice of the reaction medium. Particularly, the cyclocondensation reactions were driven by the solubility, tautomerization, or by social self-sorting. The resorcinsalens crystallized as inclusion compounds, in which the guest molecules were situated either in channels or in voids. In the highly hydrated crystals of one of the [2+2] macrocycles and chloroform-solvated crystals of a [4+4] product the channels were interconnected, as in zeolites, enabling possible migration of loosely bound solvent molecules in three dimensions. The association mode depended on the structural modification of the host molecule and the type of included solvent molecule(s).

Crystal and Molecular Structural Features of Indolin-2-One Derivatives with Sterically Hindered Phenol Moieties

The crystal and molecular structure of four indolin-2-ones with a bulky phenol substituent is studied by single crystal X-ray diffraction. All structures contain a sterically loaded 4-hydroxy-3,5-di-tert-butylbenzyl substituent at the N(1) position of the indole heterocycle. The crystal unit cells of two compounds with the thiosemicarbazone substituent at the C(3) atom of the cycle include one DMSO solvent molecule and the cells of two other molecules with the oxygen atom at the same position do not include solvent molecules. In two of the studied structures the thiosemicarbazone moiety has the Z,E,E configuration favorable for manifestation of the biological activity of these compounds. In three of four molecules the OH group of the bulky substituent at the N(1) atom of the cycle is not involved in hydrogen bonds due to steric hindrances.

Temperature‐Driven Planar Chirality Switching of a Pillar[5]arene‐Based Molecular Universal Joint

AbstractThe study of an enantiopure bicyclic pillar[5]arene‐based molecular universal joint (MUJ) by single‐crystal X‐ray diffraction allowed for the first time the unequivocal assignment of the absolute configuration of a planar chiral pillar[5]arene by circular dichroism spectroscopy. Crucially, the absolute configuration of the MUJ was switched reversibly by temperature, with an accompanying sign inversion of the anisotropy factor that varied by as much as 0.03, which is the largest value ever reported. Mechanistically, the reversible chirality switching of the MUJ is driven by the threading/dethreading motion of the fused ring and hence is dependent on both the size and nature of the ring and the solvent employed, reflecting the critical balance between the self‐complexation of the ring by pillar[5]arene, the solvation to the excluded ring, and the inclusion of solvent molecules in the cavity.

Temperature-Driven Planar Chirality Switching of a Pillar[5]arene-Based Molecular Universal Joint.

The study of an enantiopure bicyclic pillar[5]arene-based molecular universal joint (MUJ) by single-crystal X-ray diffraction allowed for the first time the unequivocal assignment of the absolute configuration of a planar chiral pillar[5]arene by circular dichroism spectroscopy. Crucially, the absolute configuration of the MUJ was switched reversibly by temperature, with an accompanying sign inversion of the anisotropy factor that varied by as much as 0.03, which is the largest value ever reported. Mechanistically, the reversible chirality switching of the MUJ is driven by the threading/dethreading motion of the fused ring and hence is dependent on both the size and nature of the ring and the solvent employed, reflecting the critical balance between the self-complexation of the ring by pillar[5]arene, the solvation to the excluded ring, and the inclusion of solvent molecules in the cavity.

Trityl Group as an Crystal Engineering Tool for Construction of Inclusion Compounds and for Suppression of Amide NH···O═C Hydrogen Bonds

It has been found that ditrityl derivatives of (R,R)-N,N′-cyclohexane-1,2-diyldiacetamide and their analogues invariably form crystals that possess inclusion properties. Enantiopurity of crystals is not a prerequisite for inclusion properties. The molecules form either two- or three-component inclusion compounds, in which hosts and guests are connected by hydrogen bonds specific for the included guest molecules but always involving the carbonyl groups of the host as acceptors. The association mode of the host molecules undergoes certain changes depending on the chemical modification of the host molecule, the type of included solvent molecule (protic/nonprotic), and whether the crystals are two- or three-component. Despite the potential for hydrogen bonding of the amide groups, no direct hydrogen bonding between the amide units of the host was observed in any of the reported structures allowing classification of a trityl group as a protection group of the amide N–H functionality in crystal engineering. X-r...

Crystal Structure and Theoretical Investigation of Charge-transport Properties of Fullerene Derivatives

Herein, the structure of an o-xylene C60 monoadduct (OXCMA) having high electron mobility in solution-processed devices was studied by single-crystal X-ray analysis. The crystal of OXCMA showed a well-aligned three-dimensional network of the C60 moiety without inclusion of solvent molecules. Density functional theory (DFT) methods and hopping modeling were employed to calculate the charge carrier mobility of OXCMA with good agreement with the experimental mobility.

Novel non-covalent stable supramolecular ternary system comprising of cyclodextrin and branched polyethylenimine

The synthesis of a novel supramolecular system comprising of branched polyethylenimine and cyclodextrin, is presented. The synthesis route is based on the self-assembly phenomena with the inclusion of solvent molecules. The systems are formed by a hydrogen-bonding network and host–guest type interactions between the building blocks. It was found that the native cyclodextrin and polyethylenimine are able to form stable systems when the reaction medium constitutes a polar solvent forming host–guest type complexes with cyclodextrin. A special consideration was paid on the detailed spectroscopic analyses of the obtained water-soluble constructs, including ROESY and diffusion-ordered (DOSY) NMR spectroscopy studies. The versatility and significance of DOSY technique for the analysis of the cyclodextrin complexes and its non-covalent systems with branched polymers, were presented. It was also found that the guest molecules that were incorporated in the complexes exhibited enhanced thermal stability. The morphological details in the solid state were obtained by scanning electron microscope.Graphical

Electronic Circular Dichroism of [16]Helicene With Simplified TD-DFT: Beyond the Single Structure Approach.

The electronic circular dichroism (ECD) spectrum of the recently synthesized [16]helicene and a derivative comprising two triisopropylsilyloxy protection groups was computed by means of the very efficient simplified time-dependent density functional theory (sTD-DFT) approach. Different from many previous ECD studies of helicenes, nonequilibrium structure effects were accounted for by computing ECD spectra on "snapshots" obtained from a molecular dynamics (MD) simulation including solvent molecules. The trajectories are based on a molecule specific classical potential as obtained from the recently developed quantum chemically derived force field (QMDFF) scheme. The reduced computational cost in the MD simulation due to the use of the QMDFF (compared to ab-initio MD) as well as the sTD-DFT approach make realistic spectral simulations feasible for these compounds that comprise more than 100 atoms. While the ECD spectra of [16]helicene and its derivative computed vertically on the respective gas phase, equilibrium geometries show noticeable differences, these are "washed" out when nonequilibrium structures are taken into account. The computed spectra with two recommended density functionals (ωB97X and BHLYP) and extended basis sets compare very well with the experimental one. In addition we provide an estimate for the missing absolute intensities of the latter. The approach presented here could also be used in future studies to capture nonequilibrium effects, but also to systematically average ECD spectra over different conformations in more flexible molecules. Chirality 28:365-369, 2016. © 2016 Wiley Periodicals, Inc.

New Family of Six Stable Metals with a Nearly Isotropic Triangular Lattice of Organic Radical Cations and Diluted Paramagnetic System of Anions: κ(κ⊥)-(BDH-TTP)4MX4·Solv, where M = CoII, MnII; X = Cl, Br, and Solv = (H2O)5, (CH2X2)

A new family of six paramagnetic metals, namely, κ-(BDH-TTP)4CoCl4·(H2O)5 (I), κ-(BDH-TTP)4Co0.54Mn0.46Cl4·(H2O)5 (II), κ-(BDH-TTP)4MnCl4·(H2O)5 (III), κ⊥-(BDH-TTP)4CoBr4·(CH2Cl2) (IV), κ⊥-(BDH-TTP)4MnBr4·(CH2Cl2) (V), and κ⊥-(BDH-TTP)4MnBr4·(CH2Br2) (VI), has been synthesized and characterized by X-ray crystallography, four-probe conductivity measurements, SQUID magnetometry, and calculations of electronic structure. The newly discovered κ⊥-type packing motif of organic layers differs from the parent κ-type by a series of longitudinal shifts of BDH-TTP radical cations in the crystal structure. Salts I–VI form two isostructural groups: I–III (κ) and IV–VI (κ⊥). Salts I–III are isostructural to the previously discovered κ-(BDH-TTP)2FeIIIX4 (X = Cl, Br) even though the charge of FeX4– anions is half that of the MX42– (M = Co, Mn) anions. The tetrahedral anions are disordered in I–III but completely ordered in IV–VI. The type of included solvent molecule is solely determined by the anion size. The paramagnetic subsystem is effectively spin diluted either by anion disorder (I–III) or by spatial separation (IV–VI). The Weiss constants are virtually zero for all compounds (e.g., θ(III) = 0.0056 K, θ(V) = −0.076 K). Curie constants are dominated by anion paramagnetic centers indicating high spin states 5/2 for MnII and 3/2 for CoII with large spin–orbital coupling. All compounds retain metallic properties down to 4.2 K. There is a magnetic breakdown gap of width (w) in the chiral salts IV–VI: w(IV) > w(V) ≈ w(VI) but no gap in the centrosymmetric salts I–III. Electronic structure calculations at room temperature revealed a nearly isotropic triangular lattice in I–III and a honeycomb lattice in IV–VI with an extreme geometric spin frustration exceeding the level reported for the quantum “spin liquid” κ-(BEDT-TTF)2Cu2(CN)3.

Piezoluminescence and Liquid Crystallinity of 4,4′-(9,10-Anthracenediyl)bispyridinium Salts

Piezoluminescence and liquid crystallinity of anthracene-based bispyridinium salts were investigated in stimulus-responsive luminescent organic crystals and luminescent ionic liquid crystals. The salts possess an anthracene moiety as a fluorophore in their center, and the pyridiniums attached to the anthracene moiety are substituted with trialkoxybenzyl groups. Single crystals of the salts bearing two trimethoxybenzyl groups were obtained as solvates. Ethyl acetate, acetone, and dioxane solvates of the chlorides have almost the same crystal structures with one-dimensional channels. Grinding of the solvated crystals caused the extrusion of the included solvent molecules, which resulted in the red shifts of their fluorescence in the solid state. The dimethyl sulfoxide solvate of the hexafluorophosphate also showed piezoluminescene by grinding. Tris(octyloxy)benzyl and tris(dodecyloxy)benzyl derivatives exhibited rectangular columnar liquid crystals upon being heated for their bromide and tetrafluoroborate s...

Computation-Ready, Experimental Metal–Organic Frameworks: A Tool To Enable High-Throughput Screening of Nanoporous Crystals

Experimentally refined crystal structures for metal–organic frameworks (MOFs) often include solvent molecules and partially occupied or disordered atoms. This creates a major impediment to applying high-throughput computational screening to MOFs. To address this problem, we have constructed a database of MOF structures that are derived from experimental data but are immediately suitable for molecular simulations. The computation-ready, experimental (CoRE) MOF database contains over 4700 porous structures with publically available atomic coordinates. Important physical and chemical properties including the surface area and pore dimensions are reported for these structures. To demonstrate the utility of the database, we performed grand canonical Monte Carlo simulations of methane adsorption on all structures in the CoRE MOF database. We investigated the structural properties of the CoRE MOFs that govern methane storage capacity and found that these relationships agree well with those derived recently from a...

Large thermal hysteresis for iron(II) spin crossover complexes with N-(pyrid-4-yl)isonicotinamide.

A new series of iron(II) 1D coordination polymers with the general formula [FeL1(pina)]·xsolvent with L1 being a tetradentate N2O2(2-) coordinating Schiff-base-like ligand [([3,3']-[1,2-phenylenebis(iminomethylidyne)]bis(2,4-pentanedionato)(2-)-N,N',O(2),O(2)'], and pina being a bridging axial ligand N-(pyrid-4-yl)isonicotinamide, are discussed. The X-ray crystal structure of [FeL1(pina)]·2MeOH was solved for the low-spin state. The compound crystallizes in the monoclinic space group P21/c, and the analysis of the crystal packing reveals the formation of a hydrogen bond network where additional methanol molecules are included. Different magnetic properties are observed for the seven samples analyzed, depending on the nature of the included solvent molecules. The widest hysteresis loop is observed for a fine crystalline sample of composition [FeL1(pina)]·xH2O/MeOH. The 88 K wide thermal hysteresis loop (T1/2↑ = 328 K and T1/2↓ = 240 K) is centered around room temperature and can be repeated without of a loss of the spin transition properties. For the single crystals of [FeL1(pina)]·2MeOH, a 51 K wide hysteresis loop is observed (T1/2↑ = 296 K and T1/2↓ = 245 K) that is also stable for several cycles. For a powder sample of [FeL1(pina)]·0.5H2O·0.5MeOH a cooperative spin transition with a 46 K wide hysteresis loop around room temperature is observed (T1/2↑ = 321 K and T1/2↓ = 275 K). This compound was further investigated using Mössbauer spectroscopy and DSC. Both methods reveal that, in the cooling mode, the spin transition is accompanied by a phase transition while in the heating mode a loss of the included methanol is observed that leads to a loss of the spin transition properties. These results show that the pina ligand was used successfully in a crystal-engineering-like approach to generate 1D coordination polymers and improve their spin crossover properties.

The Extended PLATON/SQUEEZE Tool in the Context of Twinning and SHELXL2014

The completion of a single crystal structure determination is often hampered by the presence of disordered solvent molecules of crystallization. The often not interesting details of that solvent disorder and its contribution to the calculated structure factors has to be modelled in some way in order to obtain publishable results. Current refinement programs include suitable constraints and restraints for a stable refinement of a discrete disorder model. This is often the preferred procedure, in particular when charge balances and valence states are relevant. Unfortunately, a discrete disorder model is not always feasible. Examples include solvent molecules in infinite channels or structures including unknown solvents or solvent mixtures. In such cases the iterative back-Fourier transformation of the content of the disordered solvent volume in a difference density map can be attempted as the contribution to the calculated structure factors. Back-Fourier transformation of disordered solvent regions was prototyped by us nearly 25 years ago (van der Sluis & Spek, 1990) around the, at that time widely used, SHELX76 refinement program. The original reason for its development was the structure determination of a pharmaceutical that contained infinite channels filled with ridges of electron density in the difference density map rather than discrete density peaks (van der Sluis & Spek, 1990). The preliminary implementation of a successful prototype procedure (called BYPASS) was complex and found not to be easily distributable due to its dependence on many (local) ad-hoc programs. A new distributable version, compatible with the next generation refinement program SHELXL97, was implemented as the SQUEEZE tool in the program package PLATON Spek, 2009). The new SHELXL2014 refinement program allows for an even more elegant implementation of the SQUEEZE tool including the possibility to apply it also for twinned structures. Examples and restrictions will be discussed.

Steroidal Wheel-and-Axle Host Type Molecules: Insights from Awkward Shape, Conformation, Z′ > 1 and Packing

The synthesis and crystal structure of three new molecular rotors derived from levonorgestrel and norethisterone are reported. The conformation, close contacts, and shape characteristics of these molecules exhibiting Z′ = 2 and the inclusion of solvent molecules were analyzed together with the crystal structures of parent molecules retrieved from the Cambridge Structural Database. For the set of estranes studied, we confirmed that whenever an alternative conformer cannot satisfy the crystallographic symmetry, a second molecule is incorporated in the asymmetric unit resulting in conformational isomorphism (Z′ > 1). The shape of these molecules could make them interesting as potential hosts.

On the Dual Roles of Ligands in the Synthesis of Colloidal Metal Nanostructures

Eloquent routes to colloidal metal nanostructures have emerged in recent years, and a central component to any successful nanosynthesis is the initial selection of metal complexes with an appropriate ligand environment. This local ligand environment may be predetermined by the coordination complex selected as the metal precursor; however, recent studies reveal that the ligand environment of coordination complexes can be modified through exchange with other components for the synthesis that include solvent molecules, capping agents, anions, and even reducing agents. Importantly, ligands can often play multiple roles in a synthesis and direct the outcome by manipulating the rates of precursor reduction and particle coalescence, providing colloidal and facet stabilization and even serving as reducing agents themselves. This Feature Article highlights examples in which the ligand environments of metal precursors and nanoparticles contribute to product formation in multiple ways. Acknowledgment of the dual roles of ligands in nanomaterial synthesis will enable new strategies for nanostructures by decoupling the often contradictory roles of ligands.

Oxidative Stability and Initial Decomposition Reactions of Carbonate, Sulfone, and Alkyl Phosphate-Based Electrolytes

The oxidative stability and initial oxidation-induced decomposition reactions of common electrolyte solvents for batteries and electrical double layer capacitors were investigated using quantum chemistry (QC) calculations. The investigated electrolytes consisted of linear (DMC, EMC) and cyclic carbonate (EC, PC, VC), sulfone (TMS), sulfonate, and alkyl phosphate solvents paired with BF4–, PF6–, bis(fluorosulfonyl)imide (FSI–), difluoro-(oxalato)borate (DFOB–), dicyanotriazolate (DCTA–), and B(CN)4– anions. Most QC calculations were performed using the M05-2X, LC-ωPBE density functional and compared with the G4MP2 results where feasible. The calculated oxidation potentials were compared with previous and new experimental data. The intrinsic oxidation potential of most solvent molecules was found to be higher than experimental values for electrolytes even after the solvation contribution was included in the QC calculations via a polarized continuum model. The presence of BF4–, PF6–, B(CN)4–, and FSI– anions near the solvents was found to significantly decrease the oxidative stability of many solvents due to the spontaneous or low barrier (for FSI–) H- and F-abstraction reaction that followed the initial electron removal step. Such spontaneous H-abstraction reactions were not observed for the solvent complexes with DCTA– or DFOB– anions or for VC/anion, TMP/PF6– complexes. Spontaneous H-transfer reactions were also found for dimers of the oxidized carbonates (EC, DMC), alkyl phosphates (TMP), while low barrier H-transfer was found for dimers of sulfones (TMS and EMS). These reactions resulted in a significant decrease of the dimer oxidation potential compared to the oxidation potential of the isolated solvent molecules. The presence of anions or an explicitly included solvent molecule next to the oxidized solvent molecules also reduced the barriers for the oxidation-induced decomposition reaction and often changed the decomposition products. When a Li+ cation polarized the solvent in the ECn/LiBF4 and ECn/LiPF6 complexes, the complex oxidation potential was 0.3–0.6 eV higher than the oxidation potential of ECn/BF4– and ECn/PF6–.

Theoretical study of keto–enol tautomerism by quantum mechanical calculations (the QM/MC/FEP method)

In this study, the tautomeric equilibrium between the keto and enol forms has been studied for five typical ketones and aldehydes: i‐butanal, acetaldehyde, acetone, acetylacetone, and dimedone. The level of theory used in the gas‐phase calculation was Becke, three‐parameter, Lee–Yang–Parr/6‐311G(d,p)//Becke, three‐parameter, Lee–Yang–Parr/6‐31G(d). The free energies of solvation were included in the calculation by using the free‐energy perturbation method based on Monte Carlo simulation, that is, the quantum mechanical/Monte Carlo/free‐energy perturbation method. Three different models, incorporating no‐water, one‐water, and two‐waters, were adopted. The results showed that in the gas phase the addition of water molecules to the reaction mechanism caused the activation barriers (ΔG‡gas) to decrease by half relative to the water‐free mechanism, but there was no effect on the relative difference in free energy, ΔGgas. The solvation effects (ΔGsol), based on quantum mechanical/Monte Carlo/free‐energy perturbation calculations, were added to those of the gas‐phase results of the one‐water and two‐waters models. The two‐waters model produced values that were very consistent with the experimental data for all of the tautomers. The differences in the relative Gibbs free energy (ΔGrxn) were less than 1.0 kcal mol–1. In summary, the inclusion of solvent molecules in gas‐phase calculations plays a very important role in producing results consistent with experimental data. Copyright © 2012 John Wiley & Sons, Ltd.

Difficulties in applying pure Kohn–Sham density functional theory electronic structure methods to protein molecules

Self-consistency-based Kohn–Sham density functional theory (KS-DFT) electronic structure calculations with Gaussian basis sets are reported for a set of 17 protein-like molecules with geometries obtained from the Protein Data Bank. It is found that in many cases such calculations do not converge due to vanishing HOMO–LUMO gaps. A sequence of polyproline I helix molecules is also studied and it is found that self-consistency calculations using pure functionals fail to converge for helices longer than six proline units. Since the computed gap is strongly correlated to the fraction of Hartree–Fock exchange, test calculations using both pure and hybrid density functionals are reported. The tested methods include the pure functionals BLYP, PBE and LDA, as well as Hartree–Fock and the hybrid functionals BHandHLYP, B3LYP and PBE0. The effect of including solvent molecules in the calculations is studied, and it is found that the inclusion of explicit solvent molecules around the protein fragment in many cases gives a larger gap, but that convergence problems due to vanishing gaps still occur in calculations with pure functionals. In order to achieve converged results, some modeling of the charge distribution of solvent water molecules outside the electronic structure calculation is needed. Representing solvent water molecules by a simple point charge distribution is found to give non-vanishing HOMO–LUMO gaps for the tested protein-like systems also for pure functionals.

Ordered bimetallic coordination networks featuring rare earth and silver cations

Three lanthanide complexes of the ditopic ligand 3-cyanopentane-2,4-dionate (acacCN) have been synthesized and structurally characterized. Longer intermolecular contacts result in ninefold coordination of the cation in Ce(acacCN)(3)(H(2)O)(2), whereas mononuclear complexes of the same stoichiometry with coordination number eight are obtained for the smaller Eu(III) and Yb(III) cations. Reaction of these labile compounds with AgPF(6) leads to re-organization of the coordination sphere of the rare earth cations: neutral extended structures are formed in which the peripheric -CN moieties of Ln(acacCN)(4) anions coordinate to silver cations. The initially formed heterometallic networks show additional coordination of water or inclusion of solvent molecules; three different structure types, two of them as isomorphous pairs, have been characterized. In the case of Eu(III) and Yb(III), these solids are instable when stored in their mother liquor and undergo a slow aging process, finally resulting in phase pure stable and solvent-free 3D networks Ln(acacCN)(4)Ag.

Investigating the solid state hosting abilities of homo- and hetero-valent [Co7] metallocalix[6]arenes

A family of homo-valent [Co(II)(7)(OH)(6)(L(1))(6)](NO(3))(2) (1), [(MeOH)(2) is a subset of Co(II)(7)(OH)(6)(L(1))(6)](NO(3))(2) (2) (where L(1)H = 2-iminomethyl-6-methoxyphenol) and hetero-valent [(NO(3))(2) is a subset of Co(III)Co(II)(6)(OH)(6)(L(2))(6)](NO(3))·3MeCN (4) (where L(2)H = 2-iminophenyl-6-methoxyphenol) complexes possess metallic skeletons describing planar hexagonal discs. Their organic exteriors form double-bowl shaped topologies, and coupled with their 3-D connectivity, this results in the formation of molecular cavities in the solid state. These confined spaces are shown to behave as host units in the solid state for guests including solvent molecules and charge balancing counter anions. Magnetic susceptibility measurements on 2 and 4 reveal weak ferro- and ferrimagnetism, respectively. The utilisation of other Co(II) salt precursors gives rise to entirely different species including the mononuclear and trinuclear complexes [Co(II)(L(2))(2)] (5) and [Co(III)(2)Na(I)(1)(L(3))(6)](BF(4)) (6) (where L(3)H = 2-iminomethyl-4-bromo-6-methoxyphenol).