Antiparallel Orientation Research Articles

Inverse electrocaloric effect in ferroelectrics and antiferroelectrics: A phenomenological approach

The inverse electrocaloric effect observed in ferroelectric materials is an intriguing phenomenon due to the counterintuitive relation between the dipolar entropy and the applied electric field. We hereby apply a Landau phenomenological approach to calculate the polarization, the dipolar entropy, and the free energy under the applied electric field, aiming for a deeper understanding of the origin of the inverse electrocaloric effect in ferroelectric and antiferroelectric materials. We demonstrate that the antiparallel orientation of the polarization with respect to the applied electric field leads to a flattening of the free energy density minima and concomitantly a less resistive polar state against the perturbation. Consequently, the dipolar entropy increases, which in turn causes an inverse electrocaloric effect in ferroelectrics. The same mechanism has been demonstrated for the antiparallel sublattice of antiferroelectrics. Furthermore, it is shown that the flattening of free energy density causes a larger increase of the dipolar entropy in an antiparallel sublattice compared to a parallel one. Hence, antiferroelectrics exhibit an inverse electrocaloric effect.

First-principles study of the magnetic exchange forces between the RuO2 (110) surface and Fe tip.

Magnetic exchange force microscopy (MExFM) is an important experimental technique for mapping the magnetic structure of surfaces with atomic resolution relying on the spin-dependent short-range exchange interaction between a magnetic tip and a magnetic surface. RuO2 is a significant compound with applications in heterogeneous catalysis and electrocatalysis. It has been characterized recently as an antiferromagnetic (AFM) material, and its magnetism has been predicted somewhat surprisingly to play an important role in its catalytic properties. In the current study, we explore theoretically whether MExFM can visualize the magnetic surface structure of RuO2 . We use density functional theory (DFT) calculations to extract the exchange interactions between a ferromagnetic Fe tip interacting with an AFM RuO2 (110) surface, as a function of tip-surface distance and the position of the tip over the surface. Mimicking the MExFM experiment, these data are then used to calculate the normalized frequency shift of an oscillating cantilever tip versus the minimum tip-surface distance, and construct corrugation height line profiles. It is found that the exchange interaction between tip and surface is strongest for a parallel configuration of the spins of the tip and of the surface; it is weakest for an anti-parallel orientation. In a corrugation profile, this gives rise to a sizable height difference of 25 pm between the spin-up and spin-down Ru atoms in the RuO2 (110) surface at a normalized frequency shift =-10.12 fNm1/2 . The O atoms in the surface are not or hardly visible in the corrugation profile.

G-quadruplex DNA: A Longer Story.

G-quadruplexes (G4s) are distinctive four-stranded DNA or RNA structures found within cells that are thought to play functional roles in gene regulation and transcription, translation, recombination, and DNA damage/repair. While G4 structures can be uni-, bi-, or tetramolecular with respect to strands, folded unimolecular conformations are most significant in vivo. Unimolecular G4 can potentially form in sequences with runs of guanines interspersed with what will become loops in the folded structure: 5'GxLyGxLyGxLyGx, where x is typically 2-4 and y is highly variable. Such sequences are highly conserved and specifically located in genomes. In the folded structure, guanines from each run combine to form planar tetrads with four hydrogen-bonded guanine bases; these tetrads stack on one another to produce four strand segments aligned in specific parallel or antiparallel orientations, connected by the loop sequences. Three types of loops (lateral, diagonal, or "propeller") have been identified. The stacked tetrads form a central cavity that features strong coordination sites for monovalent cations that stabilize the G4 structure, with potassium or sodium preferred. A single monomeric G4 typically forms from a sequence containing roughly 20-30 nucleotides. Such short sequences have been the primary focus of X-ray crystallographic or NMR studies that have produced high-resolution structures of a variety of monomeric G4 conformations. These structures are often used as the basis for drug design efforts to modulate G4 function.We believe that the focus on monomeric G4 structures formed by such short sequences is perhaps myopic. Such short sequences for structural studies are often arbitrarily selected and removed from their native genomic sequence context, and then are often changed from their native sequences by base substitutions or deletions intended to optimize the formation of a homogeneous G4 conformation. We believe instead that G-quadruplexes prefer company and that in a longer natural sequence context multiple adjacent G4 units can form to combine into more complex multimeric G4 structures with richer topographies than simple monomeric forms. Bioinformatic searches of the human genome show that longer sequences with the potential for forming multiple G4 units are common. Telomeric DNA, for example, has a single-stranded overhang of hundreds of nucleotides with the requisite repetitive sequence with the potential for formation of multiple G4s. Numerous extended promoter sequences have similar potentials for multimeric G4 formation. X-ray crystallography and NMR methods are challenged by these longer sequences (>30 nt), so other tools are needed to explore the possible multimeric G4 landscape. We have implemented an integrated structural biology approach to address this challenge. This approach integrates experimental biophysical results with atomic-level molecular modeling and molecular dynamics simulations that provide quantitatively testable model structures. In every long sequence we have studied so far, we found that multimeric G4 structures readily form, with a surprising diversity of structures dependent on the exact native sequence used. In some cases, stable hairpin duplexes form along with G4 units to provide an even richer landscape. This Account provides an overview of our approach and recent progress and provides a new perspective on the G-quadruplex folding landscape.

RNA as a Major-Groove Ligand: RNA-RNA and RNA-DNA Triplexes Formed by GAA and UUC or TTC Sequences.

Friedreich's ataxia is associated with noncanonical nucleic acid structures that emerge when GAA:TTC repeats in the first intron of the FXN gene expand beyond a critical number of repeats. Specifically, the noncanonical repeats are associated with both triplexes and R-loops. Here, we present an in silico investigation of all possible triplexes that form by attaching a third RNA strand to an RNA:RNA or DNA:DNA duplex, complementing previous DNA-based triplex studies. For both new triplexes results are similar. For a pyridimine UUC+ third strand, the parallel orientation is stable while its antiparallel counterpart is unstable. For a neutral GAA third strand, the parallel conformation is stable. A protonated GA+A third strand is stable in both parallel and antiparallel orientations. We have also investigated Na+ and Mg2+ ion distributions around the triplexes. The presence of Mg2+ ions helps stabilize neutral, antiparallel GAA triplexes. These results (along with previous DNA-based studies) allow for the emergence of a complete picture of the stability and structural characteristics of triplexes based on the GAA and TTC/UUC sequences, thereby contributing to the field of trinucleotide repeats and the associated unusual structures that trigger expansion.

Impact of the Hydrogen-Bonding Functional Group on Hydrogelation of Amphiphilic Naphthalene-diimide Derivatives and Nonspecific Protein Adsorption.

This manuscript reports the effect of hydrogen-bonding functionality on the supramolecular assembly of naphthalene-diimide (NDI)-derived amphiphilic building blocks in water. All the molecules contain a central NDI chromophore, functionalized with a hydrophilic oligo-oxyethylene (OE) wedge in one arm and a phenyl group on the opposite arm. They differ by a single H-bonding functionality, which links the NDI chromophore and the phenyl moiety. The H-bonding functionalities are amide, thioamide, urea, and urethane in NDI-A, NDI-TA, NDI-U, and NDI-UT, respectively. All of these molecules exhibit π-stacking in water, as evident from their distinct UV/vis absorption spectra when compared to that of the monomeric dye in THF. However, among these four, only NDI-A and NDI-TA show hydrogelation, while the other two precipitate out of the medium. The NDI-A hydrogel also exhibits transient stability and leads to a crystalline precipitate within ∼5 h. Only NDI-TA produces stable transparent hydrogel with the entangled fibrillar morphology that is typical for gelators. Both NDI-A and NDI-TA showed a thermoresponsive property with a lower critical solution temperature of about 41-42 °C. Powder XRD studies show a parallel orientation for NDI-A and an antiparallel orientation for NDI-TA. Computational studies support this experimental observation and indicate that the NDI-A assembly is highly stabilized by strong H-bonding among the amide groups and π-stacking interaction in the parallel orientation. On the other hand, due to weak H-bonding among the thioamide groups, the binding energy of the parallelly oriented NDI-TA was significantly lower and the optimized structure was disordered. Instead, its antiparallel orientation was more stable, with criss-cross aligned H-bonding interactions and π-π interactions between adjacent aromatic rings. The NDI-TA hydrogel with less ordered OE chains on the surface showed prominent adsorption of serum protein BSA. In sharp contrast, NDI-A did not exhibit any notable interaction with BSA, as evident from the ITC studies.

Structural mechanism for bidirectional actin cross-linking by T-plastin

To orchestrate cell mechanics, trafficking, and motility, cytoskeletal filaments must assemble into higher-order networks whose local subcellular architecture and composition specify their functions. Cross-linking proteins bridge filaments at the nanoscale to control a network's μm-scale geometry, thereby conferring its mechanical properties and functional dynamics. While these interfilament linkages are key determinants of cytoskeletal function, their structural mechanisms remain poorly understood. Plastins/fimbrins are an evolutionarily ancient family of tandem calponin-homology domain (CHD) proteins required to construct multiple classes of actin networks, which feature diverse geometries specialized to power cytokinesis, microvilli and stereocilia biogenesis, and persistent cell migration. Here, we focus on the structural basis of actin network assembly by human T-plastin, a ubiquitously expressed isoform necessary for the maintenance of stable cellular protrusions generated by actin polymerization forces. By implementing a machine-learning-enabled cryo-electron microscopy pipeline for visualizing cross-linkers bridging multiple filaments, we uncover a sequential bundling mechanism enabling T-plastin to bridge pairs of actin filaments in both parallel and antiparallel orientations. T-plastin populates distinct structural landscapes in these two bridging orientations that are selectively compatible with actin networks featuring divergent architectures and functions. Our structural, biochemical, and cell biological data highlight inter-CHD linkers as key structural elements underlying flexible but stable cross-linking that are likely to be disrupted by T-plastin mutations that cause hereditary bone diseases.

Adhesive Wear and Frictional Performance of Banana Fibre Reinforced Epoxy (BaFRE) Composite.

This current work is an attempt to investigate the tribological performance of banana fibre-reinforced epoxy (BaFRE) composite in dry contact conditions. The test is conducted on a wear test rig of type Block on Ring (BOR) based on ASTM G77, G137-95 standard. Different applied normal loads (5–30 N) subjected to a stainless steel counterface at different sliding speeds (1.7–3.96 m/s) and fixed sliding distance of 6.72 km were set as the experimental parameters. The test was conducted using neat epoxy (NE) as the control tests’ specimen while BaFRE composite was in anti-parallel (AP) and parallel (P) fibre strips orientation (O). The specific wear rate (Ws), friction coefficient, temperature variation and surface roughness (RA) of the NE and BaFRE composite in AP-O and P-O were investigated. The worn surface morphology of the test samples was examined under a high-resolution metallurgy microscope. The outcome of the work revealed that AP-O exhibited excellent wear performance when compared to P-O and NE. Moreover, the lowest friction coefficient of 0.0121 is achieved when AP-O is subjected to 30 N of applied load and 3.96 m/s of sliding velocity. BaFRE composite in AP-O demonstrated the lowest range of temperature variation when it was subjected to 30 N at 3.96 m/s of counterface sliding velocity. Due to the high shear resistance at the rubbing zone incurred by the AP-O test specimen and counterface, the RA values were remarkably high for the test specimen (i.e., 1.122 µm) and the counterface wear track zone (0.166 µm) as compared to the P-O and NE test samples. The predominant wear mechanism for the AP-O test specimen was plastic deformation, detached fibre, micro crack, minor fibre debonding and micro ploughing. In conclusion, there are improvements in terms of wear and friction performance of the composite when banana fibres are used as a reinforced element in epoxy resin. The improvement in Ws and friction coefficient for the AP test specimen was 29.4% and 48.6%, respectively, as compared to NE at 30 N of applied load, 6.72 km of sliding distance and 2.83 m/s of sliding speed.

Reconfigurable Magnonic Crystals Based on Imprinted Magnetization Textures in Hard and Soft Dipolar-Coupled Bilayers.

Reconfigurable magnetization textures offer control of spin waves with promising properties for future low-power beyond-CMOS systems. However, materials with perpendicular magnetic anisotropy (PMA) suitable for stable magnetization-texture formation are characterized by high damping, which limits their applicability in magnonic devices. Here, we propose to overcome this limitation by using hybrid structures, i.e., a PMA layer magnetostatically coupled to a low-damping soft ferromagnetic film. We experimentally show that a periodic stripe-domain texture from a PMA layer is imprinted upon the soft layer and induces a nonreciprocal dispersion relation of the spin waves confined to the low-damping film. Moreover, an asymmetric bandgap features the spin-wave band diagram, which is a clear demonstration of collective spin-wave dynamics, a property characteristic for magnonic crystals with broken time-reversal symmetry. The composite character of the hybrid structure allows for stabilization of two magnetic states at remanence, with parallel and antiparallel orientation of net magnetization in hard and soft layers. The states can be switched using a low external magnetic field; therefore, the proposed system obtains an additional functionality of state reconfigurability. This study offers a link between reconfigurable magnetization textures and low-damping spin-wave dynamics, providing an opportunity to create miniaturized, programmable, and energy-efficient signal processing devices operating at high frequencies.

Structural Analysis of the Poly(thymidine)-Melamine Assembly.

Hydrogen bonding between the DNA nucleobases and small organic molecules, such as melamine, is a new strategy for the design of novel DNA materials. Poly(thymidine) DNA and melamine self-assemble into a duplex structure containing two antiparallel DNA strands hydrogen bonded to central melamine units. In this Article, molecular dynamics simulations rationalize the observed antiparallel duplex structure. Alternative duplex and triplex structures with parallel and antiparallel strand orientations are shown to be unstable because of the increase in unfavorable interactions between the DNA backbones.

Monolayer MnX and Janus XMnY ( X,Y=S , Se, Te): A family of two-dimensional antiferromagnetic semiconductors

We present first-principles results on the structural, electronic, and magnetic properties of a new family of two-dimensional antiferromagnetic (AFM) manganese chalcogenides, namely monolayer MnX and Janus XMnY (X, Y= S, Se, Te), among which monolayer MnSe was recently synthesized in experiments [\href{https://pubs.acs.org/doi/abs/10.1021/acsnano.1c05532}{ACS Nano 15 (8),13794 (2021)}]. By carrying out calculations of the phonon dispersion and \textit{ab-initio} molecular dynamics simulations, we first confirmed that these systems, characterized by an unconventional strongly coupled bilayer atomic structure (consisting of Mn atoms buckled to chalcogens forming top and bottom ferromagnetic (FM) planes with antiparallel spin orientation) are dynamically and thermally stable. The analysis of the the magnetic properties shows that these materials have robust AFM order, retaining a much lower energy than the FM state even for under strain. Our electronic structure calculations reveal that pristine MnX and their Janus counterparts are indirect-gap semiconductors, covering a wide energy range and displaying tunable band gaps by the application of biaxial tensile and compressive strain. Interestingly, owing to the absence of inversion and time-reversal symmetry, and the presence of an asymmetrical potential in the out-of-plane direction, Janus XMnY become spin-split gapped systems, presenting a rich physics yet to be explored. Our findings provide novel insights in this physics, and highlight the potential for these two-dimensional manganese chalcogenides in AFM spintronics.

Transmission magneto-optics in multilayers at transverse magnetization

Transverse magneto–optic (MO) effect in transmission (TMOET) in multilayers presents interest in the studies of interfaces in magnetic nanostructures and in the design of nonreciprocal devices and magnetic sensors. It can be used as an easily accessible characterization tool for layered nanostructures with antiferromagnetic ordering considered for antiferromagnetic spintronics. TMOET can provide the information on magnetic structure with sub-nanometer resolution in a dynamic regime up to THz frequencies. The approach is illustrated on TMOET in multilayered Fe/AlN systems at a radiation wavelength of 410 nm. TMOET distinguishes between parallel and antiparallel orientation of magnetic moments in layered nanostructures and can be made stronger at antiparallel orientation of magnetic moments. The TMOET response can be optimized by sandwiching the magnetic film with dielectrics and exploited in sensors of high frequency electromagnetic fields.

Simulation Investigation of Bulk and Surface Properties of Liquid Benzonitrile: Ring Stacking-Assessment and Deconvolution.

The content and the molecular dynamics (MD) simulation analysis here are inspired by our recent ab initio calculation on benzonitrile (BZN), whereas the present results are to expand and develop macroscopic documentation involving data verification. MD simulations of the bulk liquid BZN in the range of 293–323 K unravel the hydrogen bond (−C≡N···H) formation with strength in the order of ortho-H ≫ meta-H ∼> para-H. The possibility for ortho-Hs to get involved in the formation of two bonds simultaneously confirms each having σ- and π-bonding features. Accordingly, we used vast efforts for structural analysis particularly based on the deconvolution of the corresponding complex correlation functions. Specific angle-dependent correlation functions led to the recognition of the molecular stacking with a strict anti-parallel orientation. The in-plane dimer and trimer also take part in the structural recognition. A singularity, found in the trend of the simulated temperature-dependent viscosity and diffusion coefficient of liquid BZN, is centered at about 313 K and quite fascinatingly emulates the reported experiment viscosity. An interplay between a small change in the trend of density and a large change in the corresponding viscosity is a key factor in supporting the singularity. Deconvolution of the simulation results allows attributing the singularity to structural alteration involving H-bonding of different types and extent. Approaching the range of 308–313 K, an alteration between hydrogen bond formation involving mostly ortho-Hs and mixed ortho-Hs + meta-H is possible and supports the singularity.

Intermolecular interactions in binary mixtures of formamide and acetone

Trajectories from molecular dynamics simulations of binary mixtures of formamide (FA) and acetone (AT) have been analyzed across the entire concentration range by means of various pair distributions and topological network analysis techniques to probe the structure of the intermolecular interaction networks existing in these mixtures. Radial pair distributions clearly indicated H-bonding interactions between the two molecule types through acetone oxygen and the cis- and/or trans-hydrogens of formamide. Decomposition of pair energy distributions into possible intermolecular interaction types revealed that the most stable formamide-acetone dimers existing in the binary mixtures interact via an H-bonding. Orientational pair distributions have shown that both the AT-AT and the FA-FA pairs tend to adopt an antiparallel dipole orientation, as their respective pair interaction energies get smaller. And, the FA-AT pairs interacting stronger than −6.3 kcal/mol are found to adopt an orientation such that the angle between the dipole of AT and the C-N bond of FA is larger than 130°. Network neighborhood analysis evidently revealed that the formamides do not show a strong preference for either molecule types. As acetone mole fraction of the mixture is increased, the added ATs are found to be capable of substituting the formamides, to a great extent, in the region spanning their second-order neighborhood. Conversely, as formamide content of the mixture is increased, the added FAs fail to adequately substitute the ATs in the region spanning their second-order neighborhood. Guided by our molecular dynamics based observations regarding the different types of intermolecular interactions existing between formamide and acetone, five FA-AT dimeric structures are highlighted. Their interaction energies are computed with density functional theory at the mPW2PLYP/def2-TZVP level. The most stable dimer is found to have an interaction energy of −7.5 kcal/mol, to involve an O⋯HC hydrogen-bonding, and to have nearly coplanar formamide and acetone. In addition, the DFT structures and interaction energies of trimers of the form AT⋯FA⋯AT and FA⋯AT⋯FA are also reported.

Dipole-dipole interactions of sulfone groups as a tool for self-assembly of a 2D Covalent Organic Framework derived from a non-linear diboronic acid

The utility of the nonlinear diboronic acid 2 , obtained from 3,7-dibromodibenzo[ b , d ]thiophene 5,5-dioxide 1 , for the preparation of Covalent Organic Frameworks was investigated. Despite significant deviation of boronic groups in 2 from the colinear arrangement, a highly crystalline porous material DBSO-COF was obtained by dehydrative polycondensation with 2,3,6,7,10,11-hexahydroxytriphenylene (HHTP) using a solvothermal approach. Subsequent PXRD studies supported by periodic DFT modelling revealed the formation of the 2D honeycomb-type lattice with eclipsed stacking model. The antiparallel orientation of neighboured layers is strongly favoured owing to dipole-dipole and C – H⋯O interactions of sulfone moieties. This gives the net stabilization energy of 45 kJ mol −1 per single sulfone motif, being primarily responsible for the effective formation of the ordered network and strongly contributing to its thermodynamic stability. The morphology was analyzed by SEM which revealed that the material forms uniform in size ca. 40 × 150 nm rod-like nano-crystallites. The Grand Canonical Monte Carlo (GCMC) simulation performed on a single nanoparticle of DBSO-COF allowed to reproduce the experimental isotherm. It also showed that N 2 molecules are mostly located close to the C – H bonds, while they are repulsed by sulfone groups. Apart from increasing the scope of useful boronic linkers beyond centrosymmetric structures, it was demonstrated that the presence of guest molecules in a porous network should be taken into account in order to obtain a more accurate prediction of porosity parameters. A highly crystalline porous Covalent Organic Framework was obtained from the nonlinear diboronic acid derived from dibenzo[ b , d ]thiophene 5,5-dioxide. The structure is precisely controlled by strong dipole-dipole and C–H⋯O S interactions of sulfone groups. • Development of a highly crystalline COF derived from a non-linear diboronic acid. • Precise structure control by dipole-dipole and HB interactions of sulfone groups. • Classical and periodic DFT approach to quantify the interactions between layers. • GCMC simulation of N2 sorption performed for a single nanoparticle.

Structural characterization of the homotropic cooperative binding of azamulin to human cytochrome P450 3A5

Cytochrome P450 3A4 and 3A5 catalyze the metabolic clearance of a large portion of therapeutic drugs. Azamulin is used as a selective inhibitor for 3A4 and 3A5 to define their roles in metabolism of new chemical entities during drug development. In contrast to 3A4, 3A5 exhibits homotropic cooperativity for the sequential binding of two azamulin molecules at concentrations used for inhibition. To define the underlying sites and mechanisms for cooperativity, an X-ray crystal structure of 3A5 was determined with two azamulin molecules in the active site that are stacked in an antiparallel orientation. One azamulin resides proximal to the heme in a pose similar to the 3A4–azamulin complex. Comparison to the 3A5 apo structure indicates that the distal azamulin in 3A5 ternary complex causes a significant induced fit that excludes water from the hydrophobic surfaces of binding cavity and the distal azamulin, which is augmented by the stacking interaction with the proximal azamulin. Homotropic cooperativity was not observed for the binding of related pleuromutilin antibiotics, tiamulin, retapamulin, and lefamulin, to 3A5, which are larger and unlikely to bind in the distal site in a stacked orientation. Formation of the 3A5 complex with two azamulin molecules may prevent time-dependent inhibition that is seen for 3A4 by restricting alternate product formation and/or access of reactive intermediates to vulnerable protein sites. These results also contribute to a better understanding of sites for cooperative binding and the differential structural plasticity of 3A5 and 3A4 that contribute to differential substrate and inhibitor binding.

Manipulation of polarized magnon transmission in a trilayer magnonic spin valve

Tunable magnon propagation is essential for constructing magnonic devices. The magnonic spin-valve effect was recently realized in a magnetic bilayer heterostructure. Similar to a standard electronic spin valve, switching from parallel to antiparallel magnetic orientations in the bilayer achieves comparatively high and low polarized magnon transmission. Here, we propose a trilayer magnonic spin-valve structure to improve controllability over polarized magnon propagation. In addition to high and low magnon transmission, we find a medium magnon transmission behavior, where magnons from the bottom layer jump across the middle magnetic layer and land in the top layer. Coupled magnon modes in the trilayer structure give rise to the magnon transmission feature. We investigate the effects of the external magnetic field and spin-orbit torque, and we can drive a $150%$ change in the medium transmission without magnetization reversal. This effect avoids the slow reversal process and increases the trilayer valve's flexibility. These findings render the possibility of dynamically manipulable magnonic information devices with multiple output states.

Association and solubility of chlorophenols in CCl4: MIR/NIR spectroscopic and DFT study

This work provides new information on the effect of position and number of substituents on association and solubility of chlorophenols in CCl4. Using MIR and NIR spectroscopy we examined solutions of 12 chlorophenols at several concentrations. In addition, we calculated (DFT) theoretical spectra and structures of monomers and associates of chlorophenols from dimer to tetramer. The number of substituents at positions 2 and 6 allows to divide studied chlorophenols into three Groups: I (3; 4; 3,4; 3,5), II (2; 2,3; 2,4; 2,5; 2,4,5), and III (2,6; 2,4,6; 2,3,4,5,6). An equilibrium between intermolecular OH⋅⋅⋅OH and intramolecular OH⋅⋅⋅Cl hydrogen bonding depends on position and number of substituents. The extent of association decreases in going from Group I to Group III due to growing steric hindrance near the OH group and the resonance effect from Cl. In chlorophenols of Group I, Cl at positions 3 or 5 weakens the OH⋅⋅⋅OH intermolecular hydrogen bonding, while for Group II it strengthens the OH⋅⋅⋅⋅Cl intramolecular bonding. In contrast, Cl at position 4 has minor effect on association. In the case of Group I, increasing concentration shifts the equilibrium towards solute–solute interactions, whereas for Groups II and III dominate the species with intramolecular OH⋅⋅⋅Cl bonding. The theoretical calculations predict that for monosubstituted chlorophenols of Group I the most stable are non-planar cyclic tetramers, while for disubstituted ones, the non-planar cyclic tetramers and linear trimers have similar binding energies. Chlorophenols of Group II prefer the cyclic non-planar trimers, whereas those of Group III form the planar dimers with an antiparallel orientation of the OH groups. Our study reveals that chlorophenols creating the cyclic associates are better soluble in CCl4 as compared with those forming the linear ones. Hence, one can conclude that in an inert or weakly interacting solvents the solubility is closely related to the structure of the solute associates.

Influence of Hydrogen Bonds and π–π Interactions on the Fluorescence of Crystalline (N-Alkylpyridyl)enamino-pyrrolo[2,3-b]quinoxalin-2-one Derivatives

This paper presents the relationship between the fluorescent properties of (E/Z)-(N-alkylpyridyl)enamino-pyrrolo[2,3-b]quinoxalin-2-one derivatives in the crystalline state and the molecular packing governed by the conformation of the molecules, hydrogen bonding, and π–π interactions. In particular, the type of 2-pyridyl alkyl chain (2-Py(CH2)n with n = 0,1,2) is responsible for the molecular packing and influences the fluorescence properties of crystalline pyrrolo[2,3-b]quinoxalines. The molecules studied exhibit permanent dipole moments that, in the crystalline phases, promote either the formation of dimers with an antiparallel orientation or stacks with a parallel dipole moment orientation. In dimers and stacks, the main observed interaction is the π–π type. The conformations of both (E)- and (Z)-enamines are stabilized by intramolecular hydrogen bonds from the NH group of the enamine to either the nitrogen atom N4 of the quinoxaline (E)-diastereoisomer or the oxygen atom of the amide carbonyl group in the (Z)-diastereoisomer. When an additional intramolecular hydrogen bond from the enamine NH group to the pyridyl nitrogen atom forms, it affects the conformation of the molecules, causing the reorientation of the molecular permanent dipole moment. Density functional theory (DFT) calculations performed for two neighboring molecules in dimers or stacks indicate two charge transfer mechanisms: intra- and intermolecular mechanisms. For centrosymmetric dimers, charge transfer occurs within each component molecule (intramolecular charge transfer). For stacks with molecules arranged by translation and noncentrosymmetric dimers, charge transfer is of an intermolecular nature. Higher absolute fluorescence quantum yields (Φf = 12.06–13.77%) are exhibited by the (E-diastereoisomers, which contain methylene or ethylene chains and form either translational stacks of the molecules or noncentrosymmetric dimers. The lowest absolute fluorescence quantum yields (Φf = 3.80–4.00%) are typical for the centrosymmetric dimers present in crystalline (Z)-(N-pyridyl)enaminopyrrolo[2,3-b]quinoxaline and (E)-(N-ethylpyridyl)enamino-pyrrolo[2,3-b]quinoxaline. The fluorescence liftimes τ were determined for single crystals of the studied phases (from 13.3 to 15.6 ns) and revealed one single process of radiative energy transfer.

Xylan adsorption on cellulose: Preferred alignment and local surface immobilizing effect

Interaction between xylan and cellulose microfibrils is required to maintain the integrity of secondary cell walls. However, the mechanisms governing their assembly and the effects on cellulose surface polymers are not fully clear. Here, molecular dynamics simulations are used to study xylan adsorption onto hydrated cellulose fibrils. Based on multiple spontaneous adsorption simulations it is shown that an antiparallel orientation is thermodynamically preferred over a parallel one, and that adsorption is accompanied by the formation of regular but orientation-dependent hydrogen bond patterns. Furthermore, xylan adsorption restricts the local dynamics of the adjacent glucose residues in the surface layer to a level of the crystalline core, which is manifested as a three-fold increase in their 13C NMR T1 relaxation time. These results suggest that xylan forms a rigid and ordered layer around the cellulose fibril that functions as a transition phase to more flexible and disordered polysaccharide and lignin domains.

Direct observation of folded human telomeric i-motif at neutral pH by single-molecule FRET

i-Motifs are four stranded DNA structures comprised of parallel-stranded DNA duplexes connected in an anti-parallel orientation by intercalated, cytosine-cytosine base pairs. They are stabilised under acidic conditions by C-C base pairing formed via hemi-protonation of the N3; folding is rapid and this property has been utilised in many nanotechnological applications. Sequences which fold into i-motifs are also prevalent across the human genome and are enriched in regions related to control of gene expression.