Water-Stable Pillared Three-Dimensional Zn-V Bimetal-Organic Framework for Promoted Electrocatalytic Urea Oxidation

Urea oxidation reaction (UOR) is one of the potential routes in which urea-rich wastewater is used as a source of energy for hydrogen production. Metal-organic frameworks (MOFs) have promising applications in electrocatalytic processes, although there are still challenges in identifying the MOFs' molecular regulation and obtaining practical catalytic systems. The current study sought to synthesize [Zn6(IDC)4(OH)2(Hprz)2]n (Zn-MOF) with three symmetrically independent Zn(II) cations connected via linear N-donor piperazine (Hprz), rigid planar imidazole-4,5-dicarboxylate (IDC3-), and -OH ligands, revealing the 3,4T1 topology. The optimized noble-metal-free Zn0.33V0.66-MOF/NF electrocatalysts show higher robustness and performance compared to those of the parent Zn monometallic MOF/NF electrode and other bimetallic MOFs with different Zn-V molar ratios. The low potential of 1.42 V (vs RHE) at 50 mA cm-2 in 1.0 M KOH with 0.33 M urea required by the developed Zn0.33V0.66-MOF electrode makes its application in the UOR more feasible. The availability of more exposed active sites, ion diffusion path, and higher conductivity result from the distinctive configuration of the synthesized electrocatalyst, which is highly stable and capable of synergistic effects, consequently enhancing the desired reaction. The current research contributes to introducing a practical, cost-effective, and sustainable solution to decompose urea-rich wastewater and produce hydrogen.

Flattening of a Bent Sulfonated MOF Linker: Impact on Structures, Flexibility, Gas Adsorption, CO2/N2 Selectivity, and Proton Conduction

Rational design of organic building blocks provides opportunities to control and tune various physicochemical properties of metal-organic frameworks (MOFs), including gas handling, proton conduction, and structural flexibility, the latter of which is responsible for new adsorption phenomena and often superior properties compared to rigid porous materials. In this work, we report synthesis, crystal structures, gas adsorption, and proton conduction for a flexible two-dimensional cadmium-based MOF (JUK-13-SO3H-SO2) containing a new sulfonated 4,4'-oxybis(benzoate) linker with a blocking SO2 bridge. This two-dimensional (2D) MOF is compared in detail with a previously reported three-dimensional Cd-MOF (JUK-13-SO3H), based on analogous, but nonflat, SO2-free sulfonated dicarboxylate. The comprehensive structure-property relationships and the detailed comparisons with insights into the networks flexibility are supported by five guest-dependent structures determined by single-crystal X-ray diffraction (XRD), and corroborated by spectroscopy (IR, 1H NMR), powder XRD, and elemental/thermogravimetric analyses, as well as by volumetric adsorption measurements (for N2, CO2, H2O), ideal adsorbed solution theory (IAST), density-functional theory (DFT+D) quantum chemical and grand-canonical Monte Carlo (GCMC) calculations, and electrochemical impedance spectroscopy (EIS) studies. Whereas both dynamic MOFs show moderate proton conductivity values, they exhibit excellent CO2/N2 selectivity related to the capture of CO2 from flue gases (IAST coefficients for 15:85 mixtures are equal to ca. 250 at 1 bar and 298 K). The presence of terminal sulfonate groups in both MOFs, introduced using a unique prechlorosulfonation strategy, is responsible for their hydrophilicity and water-assisted proton transport ability. The dynamic nature of the MOFs results in the appearance of breathing-type adsorption isotherms that exhibit large hysteresis loops (for CO2 and H2O) attributed to strong host-guest interactions. Theoretical modeling provides information about the adsorption mechanism and supports interpretation of experimental CO2 adsorption isotherms.

Comparative Analysis of Vegetable and Mineral Oil-Based Antiadhesive/Hydrophobic Liquids and Their Impact on Wood Properties

The unavailability of biodegradable preservatives is one of the major setbacks in the construction industry. With this in mind, our study focused on the analysis and comparison of two hydrophobic liquids, one vegetable oil-based (VOA) and the other mineral oil-based (MOA), and subsequently applying the same on three types of wood. The comparison of the vegetable oil-based (VOA) and mineral oil-based (MOA) hydrophobic liquids revealed that VOA was characterized by an 83.4% susceptibility to aerobic biodegradation, while MOA was considerably more resistant (47.80%). Based on the conducted contact angle measurements, it was observed that the wettability of pine and oak wood decreased after the application of both VOA (for pine-twice; for oak-by 38%) and MOA (for pine-more than two times; for oak-by 49%), while in the case of aspen, the same was increased (after the application of VOA-by 20%; after the application of MOA-by 2%). The observed depth of penetration into the structure of the impregnated wood was lower for the VOA impregnant as compared to the MOA impregnant. This result persisted in all types of wood used in the experiment. Observations of the process of water absorption during soaking revealed that VOA was more beneficial in terms of lowering water absorption into the material, regardless of wood type. The overall results were better for VOA, which lowered the mass of soaked wood by between 19.73 and 66.90%.

A building-block database of distributed polarizabilities and dipole moments to estimate optical properties of biomacromolecules in isolation or in an explicitly solvated medium

Since atomic or functional-group properties in the bulk are generally not available from experimental methods, computational approaches based on partitioning schemes have emerged as a rapid yet accurate pathway to estimate the materials behavior from chemically meaningful building blocks. Among several applications, a comprehensive and systematically built database of atomic or group polarizabilities and related opto-electronic quantities would be very useful not only to envisage linear or non-linear optical properties of biomacromolecules but also to improve the accuracy of classical force fields devoted to simulate biochemical processes. In this work, we propose the first entries of such database that contains distributed polarizabilities and dipole moments extracted from fragments of peptides. Twenty three prototypical conformers of the dipeptides alanine-alanine and glycine-glycine were used to extract functional groups such as CH₂ , CHCH₃ , NH₂ , COOH, CONH, thus allowing construction of a diversity of chemically relevant environments. To evaluate the accuracy of our database, reconstructed properties of larger peptides containing up to six residues of alanine and glycine were tested against density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory. The procedure is particularly accurate for the diagonal components of the polarizability tensor with errors up to 15%. In order to include solvent effects explicitly, the peptides were also surrounded by a box of water molecules whose distribution was optimized using the CHARMM force field. Solvent effects introduced by a classical dipole-dipole interaction model were compared to those obtained from polarizable-continuum model calculations.

The nature of π-hole interactions between iodide anions and quinoid rings in the crystalline state

The investigated co-crystal of 3-chloro-N-methylpyridinium iodide with tetrabromoquinone (3-Cl-N-MePy·I·Br₄Q) reveals a π-hole interaction between an iodide anion and a quinoid ring involving an n → π* charge transfer. The quinoid ring has a partial negative charge (estimated to be in the range 0.08-0.11e) and a partial radical character, which is related to the black colour of the crystals (crystals of neutral tetrabromoquinone are yellow). A detailed X-ray charge density study revealed two symmetry-independent bond critical points between the iodide anions and carbon atoms of the ring. Their maximum electron density of 0.065 e Å^-3 was reproduced by quantum chemical modelling. The energy of the interaction is estimated to be -11.16 kcal mol^-1, which is comparable to the strength of moderate hydrogen bonding (about -10 kcal mol^-1); it is dominantly electrostatic in nature, with a considerable dispersion component.

Structure Elucidation of Lithium Compounds Using 7 Li Residual Quadrupolar Couplings

A new NMR method for the structure elucidation of lithium compounds under solution-like conditions is presented. It is based on the measurement of ⁷ Li residual quadrupolar couplings (RQCs) in a stretched polystyrene (PS) gel, and comparison to RQCs predicted from crystal or DFT-derived model structures in combination with alignment tensors derived from one-bond ¹ H,¹³ C residual dipolar couplings (RDCs). The method was applied to five lithium model complexes containing monoanionic, bidentate bis(benzoxazole-2-yl)methanide, bis(benzothiazole-2-yl)methanide and bis(pyridyl)methanide ligands, of which two are first introduced in this work. In agreement with the crystalline state, four complexes are monomeric with Li coordinated fourfold by two additional THF molecules, whereas in one complex bulky tBu groups only provide space for one additional THF molecule.

Hierarchical analysis of the target-based scoring function modification for the example of selected class A GPCRs

Computational methods, especially molecular docking-based calculations, have become indispensable in the modern drug discovery workflow. The constantly increasing chemical space requires fast, robust but most of all highly predictive methods to search for new bioactive agents. Thus, the scoring function (SF) is a useful and broadly applied energy-based element of docking software, allowing quick and effective evaluation of a ligand's propensity to bind to selected protein targets. Despite many spectacular successes of molecular docking applications in virtual screening (VS), the obtained results are often far from ideal, leading to incorrect selection of hit molecules and poor pose prediction. In our study we focused on docking calculation for the selected class A G-protein coupled receptors (GPCRs), with experimentally determined 3D structures and a sufficient set of known ligands with affinity values reported in the ChEMBL database. Our goal is to investigate how much the energy-based scoring function for this particular target class changes when changing from the default to the re-estimated weighting scheme on the specified energy terms in the SF definition. Additionally, we want to verify if indeed more accurate results are obtained when considering different levels of the biological hierarchy, namely: the whole class A GPCRs, sub-subfamilies, or just the individual proteins while applying default or specifically designed weighting coefficients. The performed calculation and evaluation factor values suggest a significant improvement of docking results for the designed SF definition. This individual approach improves the accuracy of binding affinity prediction and active compound recognition. The designed scoring function for classes, sub-subfamilies, or proteins leads to a significant improvement of molecular docking performance, especially at the level of individual proteins. Our results show that to increase the efficiency and predictive power of molecular docking calculations applied in classical VS, the strategy based on the individual approach for scoring function definition for selected proteins should be considered.

Benchmark of a functional-group database for distributed polarizability and dipole moment in biomolecules

The extraction of functional-group properties in condensed phases is very useful for predicting material behaviors, including those of biomaterials. For this reason, computational approaches based on partitioning schemes have been developed aiming at rapidly and accurately estimating properties from chemically meaningful building blocks. A comprehensive database of group polarizabilities and dipole moments is useful not only to predict the optical properties of biomacromolecules but also to improve molecular force fields focused on simulating biochemical processes. In this work we benchmark a database of distributed polarizabilities and dipole moments for functional groups extracted from a series of polypeptides. This allows reconstruction of a variety of relevant chemical environments. The accuracy of our database was tested to predict the electro-optical properties of larger peptides and also simpler amino acids for which density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory was chosen as the reference. This approach is reasonably accurate for the diagonal components of the polarizability tensor, with errors not larger than 15-20%. The anisotropy of the polarizability is predicted with smaller efficacy though. Solvent effects were included explicitly by surrounding the database entries by a box of water molecules whose distribution was optimized using the CHARMM force field.

Plant Material as a Novel Tool in Designing and Formulating Modern Biostimulants-Analysis of Botanical Extract from Linum usitatissimum L

Nowadays, researchers are looking into next-generation biostimulants that can be designed as a dedicated agronomic tool based on plant materials. The aim of the present study was to develop a novel biostimulating product, based on plant material in the form of linseed aqueous extracts. The scope of the research included the physicochemical characterization of the product and identification of its biostimulating potential. The study has confirmed that the plant biostimulant derived from L. usitatissimum can be used as a viable agronomic tool for growing soybean. The designed and produced biostimulant is rich in bioactive compounds, including amino acids, free fatty acids, carbohydrates, and micro- and macroelements. The tested biostimulant showed significantly lower values of surface tension in relation to water and a commercial biostimulant. The soybean crops responded to the application of the preparation by improvements in agronomic and morphological levels. The linseed macerates were effective in terms of soybean yields and profitability. Our findings serve as preliminary evidence for the viability of designing and developing novel biostimulants derived from plant materials. This comprehensive approach to designing and formulating novel bioproducts necessitates more extensive and targeted research to fully explain the mechanisms behind the improvements observed in the soybean cultivation.

Charge density studies of multicentre two-electron bonding of an anion radical at non-ambient temperature and pressure

The variation of charge density of two-electron multicentre bonding (pancake bonding) between semi-quinone radicals with pressure and temperature was studied on a salt of 5,6-di-chloro-2,3-di-cyano-semi-quinone radical anion (DDQ) with 4-cyano-N-methyl-pyridinium cation (4-CN) using the Transferable Aspheric Atom Model (TAAM) refinement. The pancake-bonded radical dimers are stacked by non-bonding π-interactions. With rising pressure, the covalent character of interactions between radicals increases, and above 2.55 GPa, the electron density indicates multicentric covalent interactions throughout the stack. The experimental charge densities were verified and corroborated by periodic DFT computations. The TAAM approach has been tested and validated for atomic resolution data measured at ambient pressure; this work shows this approach can also be applied to diffraction data obtained at pressures up to several gigapascals.

Accurate Atom-Dipole Interaction Model for Prediction of Electro-optical Properties: From van der Waals Aggregates to Covalently Bonded Clusters

This work aims at the accurate estimation of the electro-optical properties of atoms and functional groups in organic crystals. A better understanding of the nature of building blocks and the way they interact with each other enables more efficient prediction of self-assembly, and thus physical properties in condensed matter. We propose a modified version of an atom-dipole interaction model that is based on atomic dipole moments calculated from the quantum theory of atoms in molecules. The method is very reliable for the prediction of various optical and electric properties in diverse chemical environments, ranging from hydrocarbon molecules bonded by dispersive interactions to polar rings connected by hydrogen bonds, or even polymeric structures whose monomers are covalently linked. Distributed polarizabilities and electrostatic potentials are compared to those obtained using a complete quantum-mechanical approach on finite-size aggregates. Our electrostatic approximation recovers isotropic polarizabilities with an accuracy of ca. 5 au and electrostatic potentials of ca. 0.05 au, even in the worst-case scenario in which polarization and charge-transfer effects are large. Functional groups are highly exportable, estimating the properties of small peptides and polyaromatics with a maximum deviation as low as ca. 15%.

Crystal structure, vibrational frequencies and polarizability distribution in hydrogen-bonded salts of pyromellitic acid

Structural features of moderate-to-strong O—H...O hydrogen bonds are related to the frequencies of O—H stretching vibrations and to the electric polarizability distribution in the donor and acceptor functional groups for crystals synthesized from the 1,2,4,5-benzenetetracarboxylic (pyromellitic) acid, namely: bis(3-aminopyridinium) dihydrogen pyromellitate tetrahydrate, (1); bis(3-carboxypyridinium) dihydrogen pyromellitate, (2); bis(3-carboxyphenylammonium) dihydrogen pyromellitate dihydrate, (3); and bis(4-carboxyphenylammonium) dihydrogen pyromellitate, (4). A combination of single-crystal X-ray diffraction, powder Raman spectroscopy and first-principle calculations in both crystalline and gaseous phases has shown that changes in the O—H...O hydrogen-bond geometry can be followed by changes in the corresponding spectral modes. Vibrational properties of moderate hydrogen bonds can be estimated from correlations based on statistical analysis of several compounds [Novak (1974).Struct. Bond.18, 177–216]. However, frequencies related to very short O—H...O bonds can only be predicted by relationships built from a subset of structurally similar systems. Moreover, the way in which hydrogen bonds affect the polarizability of donor and acceptor groups depends on their strength. Moderate interactions enhance the polarizability and make it more anisotropic. Shorter hydrogen bonds may decrease the polarizability of a group as a consequence of the volume restraint implied by the neighbour molecule within a hydrogen-bonded aggregate. This is significant for evaluation of the electric susceptibility in crystals and, therefore, for estimation of refractive indices and birefringence.

Collective Breathing in an Eightfold Interpenetrated Metal-Organic Framework: From Mechanistic Understanding towards Threshold Sensing Architectures

Functional materials that respond to chemical or physical stimuli through reversible structural transformations are highly desirable for the integration into devices. Now, a new stable and flexible eightfold interpenetrated three-dimensional (3D) metal-organic framework (MOF) is reported, [Zn(oba)(pip)]_n (JUK-8) based on 4,4'-oxybis(benzenedicarboxylate) (oba) and 4-pyridyl functionalized benzene-1,3-dicarbohydrazide (pip) linkers, featuring distinct switchability in response to guest molecules (H₂ O and CO₂ ) or temperature. Single-crystal X-ray diffraction (SC-XRD), combined with density functional theory (DFT) and grand canonical Monte Carlo (GCMC) simulations, reveal a unique breathing mechanism involving collective motions of eight mixed-linker diamondoid subnetworks with only minor displacements between them. The pronounced stepwise volume change of JUK-8 during water adsorption is used to construct an electron conducting composite film for resistive humidity sensing.

One-step introduction of terminal sulfonic groups into a proton-conducting metal–organic framework by concerted deprotonation–metalation–hydrolysis reaction

A one-step strategy for introducing terminal sulfonic groups from a hydrolysable precursor is demonstrated for a proton-conducting metal–organic framework.

Electrostatic potential and non-covalent interactions analysis for the design of selective 5-HT7 ligands

Despite the significant improvement of methodology in the field of the in silico drug discovery, the search for selective drugs is still far from trivial. This is especially relevant in the case of designing new medicaments for treatment of central nervous system disorders. In this work, we present a new approach based on the molecular docking and the following electronic properties analysis of ligands' binding poses (electrostatic potential distribution analysis and quantitative topological analysis of the electron density distribution). The proposed protocol significantly increases the success rate of the selective 5-HT₇R ligands against 5-HT_1AR selection from the prepared databases (the rise from 33.3% to 77.8% and from 22.7% to 62.5% for training and testing sets, respectively). The presented approach can be applied as a supportive method in the virtual screening of ligands databases.

Origin of chromic effects and crystal-to-crystal phase transition in the polymorphs of tyraminium violurate

Chromic materials are nowadays widely used in various technological applications, however understanding the effect and the possibility of tuning the obtained colour of a material are still challenging. Here a combined experimental and theoretical study is presented on the solvatochromic and crystallochromic effects in the (pseudo)polymorphs of tyraminium violurate. This organic material exhibits a large solvatochromic shift (ca 192 nm) associated with broad colour change (from yellow to dark violet). Tyraminum violurate crystallizes as red crystals of form (I) from water as a solvate, and as an unsolvated form [violet crystals of (II)] from methanol solution. Form (I), when heated, undergoes two crystal-to-crystal phase transformations associated with colour change of the crystals. Crystals of (II) show extreme birefringence (ca 0.46) and high refractive index (n γ above 1.90), which can be correlated with preferential orientation of the resultant dipole moments of the ions. Examination of optical effects (UV-Vis spectra) along with theoretical calculations (QTAIM, atomic and bond polarizabilities) enabled the description of the origin of colour in the studied materials.

A bio-relevant supramolecular Co(ii)-complex for selective fluorescence sensing of μM range inorganic As(iii) in aqueous medium and its intracellular tracking in bacterial systems

A bio-relevant fluorescent supramolecular Co(ii)-complex selectively detects μM range toxic inorganic As(iii) in water and in bacterial systems.

The effect of the intramolecular C–H⋯O interactions on the conformational preferences of bis-arylsulfones – 5-HT6 receptor antagonists and beyond

The development of compounds with enhanced activity and selectivity by a conserved spatial orientation of the pharmacophore elements has a long history in medicinal chemistry. Rigidified compounds are an example of this concept. However, the intramolecular interactions were seldom used as a basis for conformational restraints. Here, we show the weak intramolecular interactions that contribute to the relatively well-conserved geometry of N1-arylsulfonyl indole derivatives. The structure analysis along with quantum mechanics calculations revealed a crucial impact of the sulfonyl group on the compound geometry. The weak intramolecular C–H⋯O interaction stabilizes the mutual "facing" orientation of two aromatic fragments. These findings extend the pharmacological interpretation of the sulfonyl group role from the double hydrogen bond acceptor to the conformational scaffold based on intramolecular forces. This feature has, to date, been omitted in in silico drug discovery. Our results should increase the awareness of researchers to consider the conformational preference when designing new compounds or improving computational methods.

The impact of weak intramolecular C–H⋯O interactions on the conformational stability of bis-arylsulfones is discussed, suggesting different role of sulfonyl group in the ligand – 5HT₆ receptor interaction.

Improvement of the photosynthetic activity of Moldavian dragonhead (Dracocephalum moldavicaL.) through foliar application of a nitrophenolate–based biostimulant

Application of biostimulants instigates many physiological processes that enhance nutrition efficiency, abiotic stress tolerance, and quality traits of crops, regardless of their nutrient content. One of such preparations is Atonik which contains nitrophenol compounds naturally occurring in plant cells. Several studies have confirmed its beneficial effect on the growth, development, and improved metabolic activity of plants. Therefore, it seems advisable to investigate the effect of Atonik preparation on the photosynthetic activity of Moldavian dragonhead (Dracocephalum moldavicaL.). The reported study was carried out in 2014 in Perespa, Poland. Over the growing season, Atonik was foliar-applied at a dose of 0.3 L/ha (0.1%) and 0.6 L/ha (0.2%) by single and double spraying of plants. Chlorophyll content and nitrogen status (N) were estimated by a Chlorophyll Meter SPAD-502 Plus. The foliar application of Atonik was found to improve the efficiency of the photosynthetic apparatus and chlorophyll content in the leaves ofDracocephalum moldavicaplants, but the results were dependent on biostimulant concentration and number of its applications, and on the date of measurement. To conclude, Atonik is an environmental-friendly preparation which has a positive impact on the metabolic processes of plants.

Exploring charge density analysis in crystals at high pressure: data collection, data analysis and advanced modelling

The possibility to determine electron-density distribution in crystals has been an enormous breakthrough, stimulated by a favourable combination of equipment for X-ray and neutron diffraction at low temperature, by the development of simplified, though accurate, electron-density models refined from the experimental data and by the progress in charge density analysis often in combination with theoretical work. Many years after the first successful charge density determination and analysis, scientists face new challenges, for example: (i) determination of the finer details of the electron-density distribution in the atomic cores, (ii) simultaneous refinement of electron charge and spin density or (iii) measuring crystals under perturbation. In this context, the possibility of obtaining experimental charge density at high pressure has recently been demonstrated [Casatiet al.(2016).Nat. Commun.7, 10901]. This paper reports on the necessities and pitfalls of this new challenge, focusing on the speciessyn-1,6:8,13-biscarbonyl[14]annulene. The experimental requirements, the expected data quality and data corrections are discussed in detail, including warnings about possible shortcomings. At the same time, new modelling techniques are proposed, which could enable specific information to be extracted, from the limited and less accurate observations, like the degree of localization of double bonds, which is fundamental to the scientific case under examination.

Charge density analysis for crystal engineering

This review reports on the application of charge density analysis in the field of crystal engineering, which is one of the most growing and productive areas of the entire field of crystallography. While methods to calculate or measure electron density are not discussed in detail, the derived quantities and tools, useful for crystal engineering analyses, are presented and their applications in the recent literature are illustrated. Potential developments and future perspectives are also highlighted and critically discussed. Graphical abstractᅟ

PolaBer: a program to calculate and visualize distributed atomic polarizabilities based on electron density partitioning

This paper describes the program PolaBer, which calculates atomic polarizability tensors from electric field perturbations of a partitioned electron density distribution. Among many possible partitioning schemes, PolaBer is currently using the quantum theory of atoms in molecules and it is interfaced to programs that apply such a partitioning. The calculation of the atomic tensors follows the idea suggested by Keith [The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design, (2007), edited by C. F. Matta & R. J. Boyd. Weinheim: Wiley-VCH], which enables the removal of the intrinsic origin dependence of the atomic charge contributions to the molecular dipole moment. This scheme allows the export, within chemically equivalent functional groups, of properties calculated from atomic dipoles, such as for example the atomic polarizabilities. The software permits visualization of the tensors and calculation of straightforward optical properties of a molecule (like the molar refractive index) or a crystal (assuming the molecule in a given crystal lattice).

Polymorphism of urea-barbituric acid co-crystals

The crystal structures of three polymorphs found for the addition complex of urea and barbituric acid are described and compared. Two polymorphs are monoclinic, space groups P2(1)/c and Cc, whereas the third is triclinic, P1. The displacement of electron density towards the mesomeric forms, corresponding to the tautomeric forms of higher stability, of the barbituric acid molecule seem to influence the type of hydrogen bonds formed, which in turn determines the different packing topology in the polymorphs. While the polymorphic forms can be easily differentiated at the first-level graph-set analysis of their hydrogen-bonding patterns, a higher-level analysis enables important features of the mutual spatial arrangement of the structural components to be revealed.