Molecular modeling of layered double hydroxide intercalated with benzoate,modeling and experiment

The structure of Zn4Al2 Layered Double Hydroxide intercalated with benzencarboxylate (C6H5COO-) was solved using molecular modeling combined with experiment (X-ray powder diffraction, IR spectroscopy, TG measurements). Molecular modeling revealed the arrangement of guest molecules, layer stacking, water content and water location in the interlayer space of the host structure. Molecular modeling using empirical force field was carried out in Cerius(2) modeling environment. Results of modeling were confronted with experiment that means comparing the calculated and measured diffraction pattern and comparing the calculated water content with the thermogravimetric value. Good agreement has been achieved between calculated and measured basal spacing: d(calc) = 15.3 A and d(exp) = 15.5 A. The number of water molecules per formula unit (6H2O per Zn4Al2(OH)12) obtained by modeling (i.e., corresponding to the energy minimum) agrees with the water content estimated by thermogravimetry. The long axis of guest molecules are almost perpendicular to the LDH layers, anchored to the host layers via COO- groups. Mutual orientation of benzoate ring planes in the interlayer space keeps the parquet arrangement. Water molecules are roughly arranged in planes adjacent to host layers together with COO- groups.     

Topography of cyclodextrin inclusion complexes : Part I. Classification of crystallographic data of α-cyclodextrin inclusion complexes

The crystallographic and stoichiometric data obtained for 17 different inclusion complexes of α-cyclodextrin are reported. The cell dimensions and space-group symmetries reflect the packing arrangement of the torus-shaped host molecules and are largely determined by the size and ionic character of the guest molecules.In the series acetic acid, propionic acid, butyric acid, valeric acid, the first three complexes with α-cyclodextrin crystallize in a cage-type structure with space group P2₁2₁2₁, which is characteristic or small, non-ionic guest molecules. The valeric acid molecule seems to be too long to be accommodated in a cage structure; thus, the α-cyclodextrin molecules are arranged such that a structure consisting of parallel channels is formed. This packing is typical for the inclusion of long, thin, or ionic guest molecules. A third class of complexes with structures differing from the two described was also observed.A correlation exists between the type of inclusion complex and the volume required for a complex molecule: 1200–≈ 1400 ų for molecular guests, and 1400–1500 ų for ionic guests.     

Modelling of Aniline-Vermiculite and Tetramethylammonium-Vermiculite; Test of Force Fields

Molecular mechanics simulations in Cerius² have been used for modelling vermiculite intercalated with tetramethylammonium and aniline cations. The published structure data obtained for these intercalated structures from X-ray single crystal diffraction have been used to test the force fields and modelling strategy for organo-clays. The strategy of modelling was based on the nonbond host-guest interactions and on rigid silicate layers and rigid guest species. The rigidity of silicate layers requires that the cell parameters a, b and % are kept fixed during the energy minimisation. The energy term was set up using the nonbond interaction terms only and the Crystal Packer module in Cerius² has been used for the energy minimisation. In Crystal Packer the rigid units, i.e. the silicate layers and guest species can be translated and rotated during energy minimisation and the cell parameters c, !, and # have been varied. Three sets of Van derWaals (VDW) parameters available in Crystal Packer: Tripos, Universal and Dreiding have been used in present molecular simulations. Ab initio MP2 calculations were performed to justify the application of the force field. The best agreement of molecular mechanics simulations with both: experimental and ab initio data was obtained with the Tripos VDW parameters for both intercalates. The results of modelling are in good agreement with the experimental data as to the cell parameters and the interlayer packing. The cell parameters reported by Vahedi-Faridi and Guggenheim (1997) for tetramethylammonium-vermiculite are: c = 13.616 Å, ! = 90°, # = 97.68° ; from the present modelling we obtained: c = 13.609 Å, ! = 90.19°, # = 97.56°. Tetramethylammonium-cations are arranged in one layer in the interlayer space. One C-C edge of NC₄ tetrahedra is perpendicular to the silicate layers. The deep immersion of the methyl groups into the ditrigonal cavities suggested by Vahedi-Faridi and Guggenheim was not confirmed by modelling. Slade and Stone (1984) presented the measured cell parameters for aniline vermiculite: c = 14.89 Å, ! = 90°, # = 97°; present result is: c = 14.81 Å, ! = 90.72°, # = 96.70° for partially exchanged vermiculite and c = 14.84 Å, ! = 90.53°, # = 97.17° for fully exchanged vermiculite. The aniline cations are positioned over the ditrigonal cavities alternating in their anchoring to lower and upper silicate layer. The C-N bonds are perpendicular to layers.     

Combination of modeling and experiment in structure analysis of intercalated layer silicates

A strategy for the structure analysis of intercalated layer silicates based on a combination of modeling (i.e. force field calculations) and experiment is presented. Modeling in conjunction with experiment enables us to analyze the disordered intercalated structures of layer silicates where conventional diffraction analysis fails. Experiment plays a key role in the modeling strategy and in corroboration of the modeling results. X-ray powder diffraction and IR spectroscopy were found to be very useful complementary experiments to molecular modeling. Molecular mechanics and molecular dynamics simulations were carried out in the Cerius2 and Materials Studio modeling environments. An overview is given of the structures of layer silicates, especially smectites intercalated with various inorganic and organic guest species. Special attention is paid to the ordering of guests in the interlayer space, as it is important for the practical applications of these intercalates, where the interlayer porosity, photofunctions, etc. must be controlled. Figure Structure of montmorillonite intercalated with octadecylamine via ion-dipole interaction with the maximum concentration of guests corresponding to the monolayer arrangement of guests with basal spacing 33.3 A. The Na cations remaining in the interlayer are visualized as pink balls     

Photophysical characterization of methyl viologen ion-exchanged within a zirconium phosphate framework

The photophysical properties of 1,1′-dimethyl-4,4′dipyridinium (methyl viologen, MV²⁺) intercalated within zirconium phosphate (ZrP) were investigated. The intercalation of MV²⁺ within ZrP was achieved by ion-exchange using a hydrated form of ZrP with six water molecules per formula unit and an interlayer distance of 10.3 Å. The intercalation yields a new phase with an interlayer distance up to 10.6 Å. The MV²⁺-exchanged ZrP material was characterized using elemental analysis, XRPD and IR data. The MV²⁺-exchanged ZrP materials show a red shift in the UV-Vis spectra in contrast with solution. The photoexcitation of nitrogen purged, MV²⁺-exchanged ZrP water suspensions with UV light leads to fluorescence emission with a maximum at 337 nm. The photoexcitation of MV²⁺-exchanged ZrP suspensions without nitrogen purging yields two fluorescence emissions with maxima at 337 and 450 nm. The emission in the visible region can be attributed to a photodecomposition product. The fluorescence quantum yields indicate that the emission of MV²⁺-exchanged ZrP is of the same order of magnitude as that of MV²⁺ in water indicating a strong deactivation of the excited state by non-radiative pathways.     

Structure of the inclusion complexes of heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin with indole-3-butyric acid and 2,4-dichlorophenoxyacetic acid

The crystal structures of the complexes of heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin with indole-3-butyric acid and with 2,4-dichlorophenoxyacetic acid were studied by X-ray diffraction. The complexes crystallize in the monoclinic P2(1) space group. The host molecules are elliptically puckered and stacked along the a crystal axis, in a head-to-tail fashion, forming columns. One primary methoxy group of the host molecule of the complex with indole-3-butyric acid has the unusual trans-gauche conformation for permethylated CDs. All the secondary O-3-CH(3) methoxy groups, some secondary O-2-CH(3) and some primary methoxy groups pointing inwards the cavity enclose the indole or the 2,4-dichlorophenoxy moieties of the guest molecules inside the cavity, while the chains of the guests protrude between two adjacent host molecules of the columns. The mean planes of the indole and 2,4-dichlorophenoxy moieties of the guests are nearly perpendicular to the mean planes of the elliptical heptagons defined by the O-4n atoms of the hosts. The carboxyl group of the guests form hydrogen bonds with oxygen atoms of the host molecules or with the water molecules found in the space between the complexes of the same column.     

Montmorillonite and Beidellite Intercalated with Tetramethylammonium Cations

Molecular mechanics simulations, combined with X-ray powder diffraction and infrared spectroscopy, have been used in structure analysis of montmorillonite and beidellite intercalated with tetramethylammonium cations. A complex structure analysis provided us with the detailed structure model, including characterization of the disorder, the total sublimation energy and a charge distribution in the structure of intercalates. The calculated basal spacings (14.36 Å for TMA-montmorillonite and 14.12 Å for TMA-beidellite) are in good agreement with the experimental values (14.31 Å for TMA-montmorillonite and 14.147 Å for TMA-beidellite). Both intercalated structures exhibit positional and orientational disorder in the arrangement of TMA cations, and consequently disorder in layer-stacking. In the present work we analyse the effect of octahedral and tetrahedral substitutions in a 2:1 silicate layer on the arrangement of tetramethylammonium (TMA) cations in the interlayer space of montmorillonite and beidellite. The most significant difference between TMA-montmorillonite and TMA-beidellite is in the charge distribution on the TMA cations and silicate layer. The TMA-beidellite structure is highly polarized, the total charge on one TMA cation is +0.167 e^–, while the total charge on the TMA cation in montmorillonite is +0.050 e^–.     

Interlayer Porosity in Montmorillonite Intercalated with Keggin-like Cation Studied by Molecular Mechanics Simulation

Molecular mechanics simulation using Cerius² modeling environment have been used to investigate the structure of montmorillonite, intercalated with Keggin-like cation⁷⁺. Present work is focused to the strategy of modelling in case of intercalated layered structures and to investigation of structure parameters characterizing the interlayer porosity, that means: the interlayer distance, the position, orientation and distribution of Keggin cations in the interlayer space and the stacking of layers. Molecular simulations revealed the structure of the interlayer and led to the following conclusions: In the most stable configuration the 3-fold axis of Keggin cation is perpendicular to the silicate layer. This orientation of Keggin cations leads to the basal spacing 19.51 (10^-10 m). Energy minimization during the translation of Keggin cation along the silicate layer gives only small fluctuations of basal spacing and no correlation has been found between the shift of cation along the layers and the value of basal spacing. No systematic relationship has been found between the shift of cation and crystal energy and no systematic relationship exists between the mutual shift of two successive layers and the values of basal spacing and crystal energy. Consequently, no two-dimensional ordering of Keggin cations in the interlayer and no regular stacking of layers can be expected. X-ray diffraction diagrams obtained for montmorillonites, intercalated with Keggin cation, confirm present conclusions.     

Structure analysis of hydrotalcite intercalated with pyrenetetrasulfonate; experiments and molecular modelling

The structure of pyrenetetrasulfonate intercalated with hydrotalcite, having the formula [Zn_0.68Al_0.32(OH)₂][(C₁₆H₆O₁₂S₄)_0.08 · x H₂O], was proposed based on molecular simulations combined with experimental data (X-ray powder diffraction, thermogravimetry). Calculations were done for samples kept at various relative humidities (0%, 84%, 98%). The appropriate models were selected from comparison of calculated and measured diffraction patterns. Modelling revealed the arrangement of pyrenetetrasulfonate anions, and the positions and the amount of water molecules in the interlayer space of the host structure. The results confirmed a large variability in the arrangement of the guest species. In the sample without water molecules (0% RH), pyrenetetrasulfonate anions formed a layer at the centre of the interlayer distance. For the sample kept at 84% RH, the anions formed two layers at the thirds of the interlayer. For the sample kept at 98% RH, the anions became tilted with respect to the layered double hydroxides (LDH) layers and are less organised. Water molecules were arranged in three distinct planes: one in the middle and two at the quarters of interlayer distance. The number of water molecules obtained by the modelling basically agrees with the water content as measured by thermogravimetry. Figure Pyrenetetrasulfonate was intercalated into hydrotalcite and equilibrated at various relative humidities. Structural analysis was performed using molecular simulations based on X-ray and thermogravimetric data     

Structure analysis of montmorillonite intercalated with rhodamine B: modeling and experiment

The intercalation process and the structure of montmorillonite intercalated with [rhodamine B]+ cations have been investigated using molecular modeling (molecular mechanics and molecular dynamics simulations), X-ray powder diffraction and IR spectroscopy. The structure of the intercalate depends strongly on the concentration of rhodamine B in the intercalation solution. The presence of two phases in the intercalated structure was revealed by modeling and X-ray powder diffraction: (i) phase with basal spacing 18 A and with bilayer arrangement of guests and (ii) phase with average basal spacing 23 A and with monolayer arrangement of guests. In both phases the monomeric and dimeric arrangement can coexist in the interlayer space. Three types of dimers in the interlayer structure have been found by modeling: (i) H-dimer (head-to-head arrangement) present in the 18 A phase, (ii) sandwich type of the head-to-tail arrangement (present in the 23 A phase) and (iii) J-dimer (head-to-tail arrangement) present in the 23 A phase. Figure Montmorillonite intercalated with rhodamine B cations. On the left: phase 18 A, bilayer dimeric arrangement of guests (H-dimers). On the right: phase 23 A, monolayer arrangement of guests prepared using intercalation solution with a low concentration of rhodamine B     

Superlattice Formation of Crystal Water in Layered Double Hydroxides for Long‐Term and Fast Operation of Aqueous Rechargeable Batteries

Aqueous rechargeable batteries (ARBs) are gaining increasing attention as alternatives to conventional nonaqueous lithium ion batteries. However, finding electrode materials with competitive electrochemical properties in various aspects is challenging. Moreover, the operation mechanism of some of high performance electrode materials is not fully understood. Here, an α‐phase layered double hydroxide (α‐LDH) working in alkaline electrolytes as an ARB cathode is reported. On charge, OH^? carrier ions intercalate into the interlayer space and react with protons detached from the host structure to yield crystal water. This crystal water is then arranged in a superlattice during charging to accommodate carrier ions and stabilize the structure. The solid solution mixing of cobalt and nickel also stabilizes the structure during the wide range of redox swing of Ni from 2+ to 4+. In pairing with Fe₃O₄/Fe(OH)₂ mixture, the α‐LDH exhibits 198.0 mA h g^?1 at 3 A g^?1, 68.3% capacity retention after 10 000 cycles, and 172.5 mA h g^?1 at 1 min charge, demonstrating the promise of hydrated compounds for ARB electrodes. The present study elucidates that the arrangement of crystal water within the host framework plays a critical role in determining the electrochemical performance of the corresponding hydrated active compound in aqueous media.     

Supramolecular recognition: association of palladium molecular clefts with planar platinum complexes

The crystal structures of two new molecular recognition adducts formed between a dicationic, di-terpyridyl-Pd-Cl molecular cleft and two square planar platinum complexes are reported. In both structures, the planar platinum-containing guests are located within the molecular cleft formed by the two parallel disposed terpyridyl-Pd-Cl⁺ units of the receptor. The crystal structure of the adduct formed between the molecular cleft and a neutral platinum complex has interplanar distances between the host and guest of 3.24 Å, a distance shorter than that usually ascribed to π-stacking interaction (∼3.45 Å). The short distance is likely the result of metal-metal interaction between the host and guest. The second adduct, that between the dicationic molecular receptor and an anionic platinum complex, also bears the guest within the molecular cleft. The interplanar distances between the cationic terpyridyl-Pd-Cl units of the host and the anionic guest (3.21 and 3.29 Å) are also shorter than typical π-stacking distances but no metal-metal interaction is present. Coulombic attraction between the host and guest is believed to be responsible for the short interplanar separation. These data are discussed in relation to analogous systems that associate through π-π and metal-metal interaction.     

Molecular Mechanics Simulations in Structure Analysis of Intercalate VOPO4·2CH3CH2OH

Molecular mechanics simulations using Cerius² combined with X-ray diffraction and supported with vibrational spectroscopy have been used to investigate the layered structure of vanadyl phosphate VOPO₄ intercalated with ethanol. This intercalated structure exhibits certain degree of disorder, which affects the diffraction diagram and obstructs the conventional structure analysis based on diffraction methods only. Present structure analysis is focused to the crystal packing in the interlayer space and layer stacking in the intercalate. The bilayer arrangement of ethanol molecules in the interlayer has been found, giving the basal spacing d = 13.21 Å, experimental d-value obtained from X-ray diffraction is 13.17 Å. One half from the total number of CH₃CH₂OH molecules is anchored with their oxygens to VOPO₄ layers to complete vanadium octahedra and their orientation is not very strictly defined. The second half of ethanoles is linked with hydrogen bridges to the anchored etahanoles and sometimes also to the layer oxygens. Positions and orientations of these unachored ethanoles with respect to VOPO₄ layers exhibit certain degree of disorder, resulting in the disorder in layer stacking. Molecular mechanics simulations revealed the character of this displacement disorder in layer stacking and enabled to determine the components of the displacement vector.     

Theoretical study of conformational disorder and selective adsorption of small organic molecules in the flexible metal-organic framework material MIL-53-Fe

Many of the potential applications for metal-organic framework (MOF) materials require molecular level understanding of their adsorption of small organic molecules, which are not readily accessible from experiment. Through high-level van der Waals corrected, hybrid density functional theory calculations, we elucidate the adsorption configurations of several, representative small organic guest molecules in an archetypal flexible MOF material, MIL-53-Fe. The predicted relative energies between low-energy adsorption configurations of 1,4-benzoquinone in MIL-53-Fe are in very good agreement with the thermal transition temperatures observed experimentally and suggest that thermodynamic factors govern the precise arrangements and loading of guests in the MOF host. Experimentally observed conformational disorder of small organic molecules in MIL-53-Fe is explained by predicted multiple low-energy adsorption configurations that are comparable with the thermal energy of the guests, kT. Finally, we show that the previously observed selective adsorption of pyridine and 2,6-lutidine molecules in water by MIL-53-Fe, can be rationalised through a careful analysis of the host–guest and guest–guest interactions and is controlled by thermodynamic factors.     

Phthalimide Polymer Donor Guests Enable over 17% Efficient Organic Solar Cells via Parallel‐Like Ternary and Quaternary Strategies

Ternary strategies show over 16% efficiencies with increased current/voltage owing to complementary absorption/aligned energy level contributions. However, poor understanding of how the guest components tune the active layer structures still makes rational selection of material systems challenging. In this study, two phthalimide based ultrawide bandgap polymer donor guests are synthesized. Parallel energies between the highest occupied molecular orbitals of host and guest polymers are achieved via incorporating selnophene on the guest polymer. Solid‐state ¹⁹F magic angle spinning nuclear magnetic spectroscopy, graze‐incidence wide‐angle X‐ray diffraction, elemental transmission electron microscopy mapping, and transient absorption spectroscopy are combined to characterize the active layer structures. Formation of the individual guest phases selectively improves the structural order of donor and acceptor phase. The increased electron mobility in combination with the presence of the additional paths made by the guest not only minimizes the influence on charge generation and transport of the host system but also contributes to increasing the overall current generation. Therefore, phthalimide based polymers can be potential candidates that enable the simultaneous increase of open‐circuit voltage and short‐circuit current‐density via fine‐tuning energy levels and the formation of additional paths for enhancing current generation in parallel‐like multicomponent organic solar cells.     

Calcium Binds to LipL32, a Lipoprotein from Pathogenic Leptospira, and Modulates Fibronectin Binding

Tubulointerstitial nephritis is a cardinal renal manifestation of leptospirosis. LipL32, a major lipoprotein and a virulence factor, locates on the outer membrane of the pathogen Leptospira. It evades immune response by recognizing and adhering to extracellular matrix components of the host cell. The crystal structure of Ca²⁺-bound LipL32 was determined at 2.3 Å resolution. LipL32 has a novel polyD sequence of seven aspartates that forms a continuous acidic surface patch for Ca²⁺ binding. A significant conformational change was observed for the Ca²⁺-bound form of LipL32. Calcium binding to LipL32 was determined by isothermal titration calorimetry. The binding of fibronectin to LipL32 was observed by Stains-all CD and enzyme-linked immunosorbent assay experiments. The interaction between LipL32 and fibronectin might be associated with Ca²⁺ binding. Based on the crystal structure of Ca²⁺-bound LipL32 and the Stains-all results, fibronectin probably binds near the polyD region on LipL32. Ca²⁺ binding to LipL32 might be important for Leptospira to interact with the extracellular matrix of the host cell.     

A new self-assembled inorganic-organic hybrid layered compound containing hexarhenium cluster: [MV][{Mn(CH3OH)2}{Re6Se8(CN)6}]

A new layered compound, [MV][{Mn(CH₃OH)₂}{Re₆Se₈(CN)₆}] (1) consists of a layer alternately knitted by hexarhenium cluster and Mn complex, and MV²⁺ cations (methyl viologen dication = 1,1′-dimethyl-4,4′-bipyridilium dication) reside between the layers. The title compound 1 is the first layered framework containing cyano-hexarhenium clusters with photoactive guest molecules, MV²⁺. The MV²⁺ can be partly exchanged by H₂TMB²⁺ (N,N,N′,N′-tetramethylbenzidine dication) to form a compound [H₂TMB²⁺]_x[MV²⁺]_1−x [{Mn(CH₃OH)₂}{Re₆Se₈(CN)₆}] (2) showing an electronic interaction between the layered framework and [H₂TMB]²⁺ cation.     

Structure of the complex of heptakis(2,6-di-O-methyl)-beta-cyclodextrin with (2,4-dichlorophenoxy)acetic acid

The structure of the complex formed by heptakis(2,6-di-O-methyl)-beta-cyclodextrin and (2,4-dichlorophenoxy)acetic acid was studied by X-ray diffraction. The dichlorophenyl moiety of the guest molecule was found outside the host hydrophobic cavity in the primary methoxy groups region whereas the oxyacetic acid chain penetrates the cavity from the primary face. The host molecules stacks along the a crystal axis forming a column. In the space between three successive hosts of the column, a guest molecule is accommodated.     

Facilitated permeation of methyl viologen into chloroplasts in situ during electric pulse generation in excitable plant cell membranes

Generation of action potential (AP) in plasma membranes of characean algae has a strong impact on photoreactions occurring in chloroplasts. Under physiological conditions, AP suppresses electron transport in alkaline and acidic regions, although to a different extent; these changes are transient and reversible. In the presence of the artificial electron acceptor, methyl viologen (MV²⁺), AP-induced changes in electron transport in photosystem II become irreversible. Incubation of Chara corallina internodal cells with MV²⁺ has no effect on the chlorophyll P700 photooxidation kinetics in photosystem I reaction centers, suggesting that MV²⁺ is inaccessible for interactions with photosystem I, because its permeation into chloroplasts of a resting cell is hindered by membrane barriers. At the same time, AP generation in the presence of MV²⁺ is accompanied by irreversible modification of P700 photooxidation kinetics, as can be evidenced from differences in absorption changes at 810 and 870 nm (ΔA ₈₁₀ signals). These findings suggest that MV²⁺ permeation into chloroplasts in situ is facilitated during or after the AP generation. Similar to the ΔA ₈₁₀ signals, light-induced changes in membrane potential do not depend on the presence of MV²⁺ in the external medium until the first excitatory stimulus is applied. Electric photoresponses of the cell are irreversibly modified by AP generated in the presence of MV²⁺ at the expense of non-cyclic photosynthetic electron transport redirected to the MV²⁺ reduction. It is concluded that AP effects on chloroplast photosynthesis in situ are complex and involve permeability changes for MV²⁺ in membrane barriers of the “plasmalemma-chloroplast envelope” system.     

Interaction of l‐leucyl‐l‐leucyl‐l‐leucine thin film with water and organic vapors: receptor properties and related morphology

The ability of highly ordered tripeptide structures to keep or change their morphology in contact with organic vapors was studied. A thin film of tripeptide l ‐leucyl‐l ‐leucyl‐l ‐leucine (LLL) was prepared having microcrystals and nanocrystals on its surface, which are stable upon vacuum drying but become objects of selective morphology change after a contact with vapors of organic solvents. Fine separate LLL crystals and their agglomerates of submicron and larger dimensions were observed by atomic force microscopy and scanning electron microscopy. After saturation with guest vapors, these crystals can remain intact or change their morphology with the increase in size or complete destruction depending on the guest molecular structure. The crystals completely lose their shape after the binding of pyridine vapors. The other studied guests produce much smaller transformations or have no effect on crystal morphology despite being sorbed by solid LLL, which was shown using quartz crystal microbalance sensor. The observed size‐exclusion effect for guest sorption by LLL was found to be broken by the same guests that can change the initial crystal shape. This helps to explain the morphology changes of LLL crystals after the guest sorption and release. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.