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.     

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^–.     

Surface and interlayer structure of vermiculite intercalated with methyl viologen

Molecular modeling using empirical force field revealed the differences between the surface and interlayer arrangement of the dye guest molecules in vermiculite intercalated with the divalent methyl viologen cation (MV²⁺). Conformation and anchoring of MV²⁺ cations on the silicate layer in the interlayer space of vermiculite host structure is different from that on the crystal surface. A preferential position has been found for the anchoring of guests on the silicate layer. Anyway the arrangement of guests in the interlayer space as well as on the crystal surface exhibits a high degree of disorder due to a certain flexibility in guest molecules arrangement and first of all due to the presence of water molecules in the interlayer space. The presence of water disturbs not only the regularity in guest positions and orientations but also in conformation of guest molecules in the interlayer space of the host structure.     

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.     

Molecular Mechanics Studies of Montmorillonite Intercalated with Tetramethylammonium and Trimethylphenylammonium

The intercalation of organoammonium cations into smectite structure is the important step in the technology of non-linear optical materials. In this study we investigated the structure of montmorillonite (MMT), intercalated with two organoammonium cations : tetramethylammonium (TMA) and trimethylphenylammonium (TMPA) using molecular mechanics simulations. The studies were focused to following aspects: arrangement of organoammonium cations in the interlayer, their positions and orientation with respect to silicate layers and their anchoring to the layers. The calculated (basal) d-spacings for MMT with TMA 14.29 Å and 15.36 Å for MMT with TMPA are in good agreement with X-ray diffraction data.     

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     

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     

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.     

Mg-Al layered double hydroxide intercalated with porphyrin anions: molecular simulations and experiments

Molecular modeling in combination with powder X-ray diffraction (XRD) provided new information on the organization of the interlayer space of Mg-Al layered double hydroxide (LDH) containing intercalated porphyrin anions [5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (TPPS)]. Anion-exchange and rehydration procedures were used for the preparation of TPPS-containing LDH with an Mg/Al molar ratio of 2. Molecular modeling was carried out in the Cerius² and Materials Studio modeling environment. Three types of models were created in order to simulate the experimental XRD patterns of LDH intercalates with a TPPS loading of 70–80% with respect to the theoretical anion exchange capacity (AEC). The models represent single-phase systems with a 100% TPPS loading in the interlayer space (Type 1) and models represent the coexistence of two phases corresponding to the total exchange from 75 to 92% (Type 2). To cover other possible arrangements, models with the coexistence of both TPPS and NO₃⁻ anions in the same interlayer space were calculated (Type 3). The models are described and compared with experimental data. In all cases, guest TPPS anions are tilted with respect to the hydroxide layers, and are horizontally shifted to each other by up to one-half of the TPPS diameter. According to the energy characteristics and simulated XRD, the most probable arrangement is of Type 2, where some layers are saturated with TPPS anions and others are filled with original NO₃⁻ anions.     

Correlation between thylakoid stacking and cation-induced decrease in photosystem I electron transport at saturating light intensity

A Mg²⁺-induced decrease of the rate of photosystem I (PS I) electron transport (DCIPH₂ → methyl viologen) in thylakoids under saturated light intensities has been reported earlier (S. Bose, J. E. Mullet, G. E. Hoch, and C. J. Arntzen, 1981, Photobiochem. Photobiophys.2, 45–52). A similar effect is observed with Na⁺, although the concentration required for half-maximal inhibition was higher by about two orders of magnitude. The cation effect was gradually abolished as the thylakoids were aged by incubation at 30 °C for 6 h. The loss of cation effect on PS I electron transport rate during aging was parallel to the corresponding loss of cation effect on thylakoid stacking. The cation concentration required for thylakoid stacking and the degree of inhibition as a function of cation concentration correlated strongly with the degree of thylakoid stacking. These observations indicated that the inhibition of the rate of PS I electron transport by cations is a consequence of cation-induced stacking of thylakoid membranes. The observed inhibition of the rate of PS I electron transport is discussed in terms of two hypotheses: (i) a fraction (20–30%) of the PS I complexes is trapped in the appressed region of grana and becomes unavailable to the electron donor (DCIPH₂) and (ii) the membrane structure is altered by the cations in such a manner that the rate constant of electron donation by the donor to the electron transport chain in the thylakoid is decreased.     

Studies on Cation-induced Thylakoid Membrane Stacking, Fluorescence Yield, and Photochemical Efficiency

Trypsin digestion of photosynthetic membranes isolated from spinach (Spinacia oleracea L.) leaves eliminates the cation stimulation of chlorophyll fluorescence. High concentrations of cations protect the fluorescence yield against trypsin digestion, and the cation specificity for this protection closely resembles that required for the stimulation of fluorescence by cations. Trypsin digestion reverses cation-induced thylakoid stacking, and the time course of this effect seems to parallel that of the reversal of cation fluorescence. High concentrations of cations protect thylakoid stacking and cation-stimulated fluorescence alike. The cation stimulation of photosytem II photochemistry remains intact after trypsinization has reversed both cation-induced thylakoid stacking and fluorescence yield. It is concluded that cation-stimulated fluorescence yield, and not the cation stimulation of photosystem II photochemistry, is associated with thylakoid membrane stacking.     

The effects of cations and trypsin on extraction of chlorophyll-protein complexes by octyl glucoside

The extraction of chlorophyll-protein (CP) complexes from thylakoids by the detergent octyl glucoside is strongly affected by pretreatment of the thylakoids with trypsin or cations. In these experiments, washed thylakoids were incubated in the presence of 0.5 μm to 5 mm Mg²⁺, pelleted, and extracted with octyl glucoside (30 mm). Increasing amounts of Mg²⁺ depressed extractability of all CP complexes, but especially the chlorophyll a + b-containing light-harvesting complex (LHC). This cation effect is observed with other cations which promote thylakoid stacking (5 mm Mn²⁺ or Ca²⁺, 50 mm Na⁺). However, the effect is not merely due to stacking, since low concentrations of Mg²⁺ (0.5 μmto 0.5 mm) have a marked effect on extractability but have no effect on light scattering (OD 550 nm), an indicator of stacking. Furthermore, trypsin treatment of thylakoids stacked with 5 mm Mg²⁺ caused a significant reversal of stacking, but had little effect on extractability. Trypsin treatment of unstacked membranes resulted in increased extractability of all CP complexes, but especially of the LHC. Cation-treated membranes are also significantly different from those “stacked” at pH 4.5. While the latter do show decreased extractability, there is no change in the chlorophyll $\text{a}\text{b}$ ratio of the extract, and the membranes cannot be “unstacked” with trypsin. We conclude that octyl glucoside extractability reflects the lateral interaction of CP complexes with each other and with other components in the same plane of the membrane. It is clear that divalent cations have several effects on thylakoid membranes, not all of which are due to their ability to promote stacking.     

Investigations of intercalation in inorganic solids with layered structures: iron-57 mössbauer spectroscopy studies of size fractionated and iron-exchanged montmorillonite clays

⁵⁷Fe mössbauer spectroscopy has been used to examine some naturally occurring layer silicates in which cations located in exchange sites in the interlayer regions can be replaced by other species. The ⁵⁷Fe Mössbauer spectra recorded from differing size fractions of two types of non-exchanged and sodium-exchanged montmorillonite clays were found to be independent of the fraction size. The spectra have been interpreted in terms of the occupation by iron(III) of a heterogeneity of similar sites within the montmorillonite lattice. No justification has been obtained for computer analysis of the data in terms of more than one characterisable lattice site and no evidence has been found for the association of any iron oxyhydroxide impurity with the montmorillonite fractions.The ⁵⁷Fe Mössbauer parameters recorded from iron(III)-exchanged montmorillonite, in which iron(III) species are intercalated within the layers, show that the process is best performed at fairly low pH using low concentrations of iron(III). Failure to control such conditions can result in the formation of iron oxyhydroxides or hydrolysed iron(III) species. The preparation of iron(II)-exchanged montmorillonite was accompanied by partial oxidation of the iron(II) to iron(III).     

Effect of montmorillonite on morphology,glass transition and crystallinity of the xylitol-plasticized bionanocomposites

High amylose based nanocomposites plasticized by xylitol were prepared via twin-screw extrusion. The synergistic interaction in the xylitol-plasticized nanocomposite was studied via various characterization methods and the unique behavior of the xylitol-plasticized nanocomposite had been discussed. As revealed in the XRD and TEM results, good intercalated/exfoliated morphology had been achieved in all the nanocomposites. Furthermore, the expansion of nanoclay basal spacing was related to the xylitol/nanoclay ratio. DSC analysis clearly proved the unique crystallization process of xylitol-plasticized samples. Moreover, in the crystallization domain results, two domains sized at approximately 93.7 Å and 346 Å were found. This observation points to a two-level complex effect from two aggregate domains; one, the re-aggregation of certain number of silicate layers into domains which trap some of the amylose polymer chains, and two, the bulk drying process which combines smaller amylose crystalline domains within a larger amorphous high amylose matrix.     

First-principles study of ammonium ions and their hydration in montmorillonites

Density functional theory calculations were performed to investigate the adsorption and hydration of an ammonium ion (NH₄ ⁺) confined in the interlayer space of montmorillonites (MMT). NH₄ ⁺ is trapped in the six-oxygen-ring on the internal surface and forms a strong binding with the surface O atoms. The hydration of NH₄ ⁺ is affected significantly by the surface. Water molecules prefer the surface sites, and do not bind with the NH₄ ⁺ unless enough water molecules are supplied. Moreover, the water molecules involved in NH₄ ⁺ hydration tend to bind with the surface simultaneously. The hydration energy increases with the intercalated water molecules, in contrast to that in gas phase. In addition, the hydration leads to the extension of MMT basal spacing.

Compositional and Solvent Engineering in Dion–Jacobson 2D Perovskites Boosts Solar Cell Efficiency and Stability

Hybrid halide 2D perovskites deserve special attention because they exhibit superior environmental stability compared with their 3D analogs. The closer interlayer distance discovered in 2D Dion–Jacobson (DJ) type of halide perovskites relative to 2D Ruddlesden–Popper (RP) perovskites implies better carrier charge transport and superior performance in solar cells. Here, the structure and properties of 2D DJ perovskites employing 3‐(aminomethyl)piperidinium (3AMP²⁺) as the spacing cation and a mixture of methylammonium (MA⁺) and formamidinium (FA⁺) cations in the perovskite cages are presented. Using single‐crystal X‐ray crystallography, it is found that the mixed‐cation (3AMP)(MA_0.75FA_0.25)₃Pb₄I₁₃ perovskite has a narrower bandgap, less distorted inorganic framework, and larger Pb? I? Pb angles than the single‐cation (3AMP)(MA)₃Pb₄I₁₃. Furthermore, the (3AMP)(MA_0.75FA_0.25)₃Pb₄I₁₃ films made by a solvent‐engineering method with a small amount of hydriodic acid have a much better film morphology and crystalline quality and more preferred perpendicular orientation. As a result, the (3AMP)(MA_0.75FA_0.25)₃Pb₄I₁₃‐based solar cells exhibit a champion power conversion efficiency of 12.04% with a high fill factor of 81.04% and a 50% average efficiency improvement compared to the pristine (3AMP)(MA)₃Pb₄I₁₃ cells. Most importantly, the 2D DJ 3AMP‐based perovskite films and devices show better air and light stability than the 2D RP butylammonium‐based perovskites and their 3D analogs.     

Modeling in Structure Analysis of Vanadyl Phosphate Intercalated with 1-Alkanols

Molecular mechanics simulations supported by X-ray powder diffraction measurements have been used to investigate the structure of vanadyl phosphate intercalated with 1-alkanols C_nH_2n+1OH for n = 2, 3, 4. Modeling revealed the specific features and differences in arrangement of alkanol molecules with different chain length, depending on the relation between the parameters of active sites network and size of guest molecules. This result enabled us to explain the irregularities in dependence of basal spacing on the chain length. The comparison of experimental d_exp and calculated d_calc values of basal spacing showed the good agreement of modeling with x-ray powder diffraction. While we obtained d_calc(Univ) = 13.05 Å for vanadyl phosphate-ethanol using the Universal force field (d_exp=13.17 Å), for vanadyl phosphate-propanol and vanadyl phosphate-butanol better agreement with experiment was obtained using the Tripos force field. In the case of vanadyl phosphate-propanol the calculated basal spacing d_calc(Tripos) = 14.49 Å, compared with an experimental value of d_exp=14.36 Å. For vanadyl phosphate-butanol d_calc(Tripos) = 17.71 Å and d_exp=17.90 Å.     

Cation binding of bis(cyclic tetrapeptide). 1H n.m.r. and c.d. evidence for conformational fitting of cyclic backbone and covalent CSSC bridge

Conformational aspects of the complexation of bis(cyclic tetrapeptide), S,S′-bis[cyclo(Gly-l-hemiCys-Sar-l-Pro)] (BCGCSP) with a metal cation were studied. Binding constants of BCGCSP with several cations were determined in aqueous solution, using circular dichroism (c.d.) titration curves. The values were compared with those of two mono-cyclic tetrapeptides, cyclo[Gly-l-Cys[Bzl(OMe)]-Sar-l-Pro] and cyclo(Sar-l-Pro-Sar-l-Pro). When complexing with alkali metal cations, BCGCSP exhibits selective affinity for Rb⁺ in preference to Li⁺, Na⁺, and K⁺. Complexing with alkaline earth metal cations, the peptide binds Ba²⁺ selectively. In addition, BCGCSP shows a marked Ba²⁺/Ca²⁺ selectively compared with the other three cyclic peptides. In order to explain these characteristics, a pseudo-inclusion complex with a castanet type structure was proposed as a model of the bis(peptide)—cation complex. The c.d. band ascribed to disulphide (SS) bond transition, showed a red shift upon complex formation. From this observation, it is suggested that conformational fitting of bis(peptide) takes place by changing the geometry of the peptide backbone and covalent CSSC bridge upon complexation with a metal cation.     

Four-Stranded Intercalated Cytosine-Rich Molecules: Novel Insights into DNA Structure and Stability

Abstract

DNA fragments with stretches of cytosine residues can form four-stranded intercalated i-DNA molecules stabilized by hemiprotonated cytosine·cytosine⁺ (C·C⁺) base pairs. Intriguing features of this motif are the accomodation of base stacking that is unfavorable due to electrostatic repulsion and the close approach of phosphates in narrow grooves of the molecule. Unusual sources of stability in this structure involve sugar-base stacking and CH-O interribose short contacts between the backbones of adjacent strands.     

Molecular dynamics simulations of hydrogen storage capacity of few-layer graphene

The adsorption of molecular hydrogen on few-layer graphene (FLG) structures is studied using molecular dynamics simulations. The interaction between graphene and hydrogen molecules is described by the Lennard-Jones potential. The effects of pressure, temperature, number of layers in a FLG, and FLG interlayer spacing are evaluated in terms of molecular trajectories, binding energy, binding force, and gravimetric hydrogen storage capacity (HSC). The simulation results show that the effects of temperature and pressure can offset each other to improve HSC. An insufficient interlayer spacing (0.35 nm) largely limits the HSC of FLG because hydrogen adsorbed at the edges of the graphene prevents more hydrogen from entering the structure. A low temperature (77 K), a high pressure, a large number of layers in a FLG, and a large FLG interlayer spacing maximize the HSC.