Unveiling GruPol: Predicting Electric and Electrostatic Properties of Macromolecules via the Building Block Approach.

Understanding electrostatics and electric properties of macromolecules is crucial in uncovering the intricacies of their behavior and functionality. The precise knowledge of these properties enhances our ability to manipulate and engineer macromolecules for diverse applications, spanning from drug design to materials science. Having that in mind, we present here the GruPol database approach to characterize and accurately predict dipole moments, static polarizabilities, and electrostatic potential of proteins and their subunits. The method involves partitioning of the electron density, calculated at the M06-HF/aug-cc-pVDZ level of theory, of small peptides into predefined building blocks that are averaged over the database. By manipulating and positioning these building blocks, GruPol enables the description of proteins assembled from over nearly 100 residual entries, allowing for efficient and precise computation of the above-mentioned properties across a broad range of proteins. The database enables the user to include solvent effects as well as define protonation states on the protein's backbone to account for pH variations. The precision of the proposed scheme is benchmarked against experimental data for myoglobin species.

Current developments and trends in quantum crystallography.

Quantum crystallography is an emerging research field of science that has its origin in the early days of quantum physics and modern crystallography when it was almost immediately envisaged that X-ray radiation could be somehow exploited to determine the electron distribution of atoms and molecules. Today it can be seen as a composite research area at the intersection of crystallography, quantum chemistry, solid-state physics, applied mathematics and computer science, with the goal of investigating quantum problems, phenomena and features of the crystalline state. In this article, the state-of-the-art of quantum crystallography will be described by presenting developments and applications of novel techniques that have been introduced in the last 15 years. The focus will be on advances in the framework of multipole model strategies, wavefunction-/density matrix-based approaches and quantum chemical topological techniques. Finally, possible future improvements and expansions in the field will be discussed, also considering new emerging experimental and computational technologies.

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%.

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.

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.

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.

Distributed functional-group polarizabilities in polypeptides and peptide clusters toward accurate prediction of electro-optical properties of biomacromolecules.

CONTEXT: Aiming at accurately predicting electro-optical properties of biomolecules, this work presents distributed atomic and functional-group polarizability tensors for a series of polypeptides and peptide clusters constructed from glycine and its residuals. By partitioning the electron density using the quantum theory of atoms in molecules, we demonstrated a very good transferability of the group polarizabilities. We were able to identify and extract the most efficient functional groups capable of generating the largest electrical susceptibility in condensed phases. Both the isotropic polarizability and its anisotropy were used to understand the way functional groups act as sources of linear optical responses, how they interact with each other reinforcing the macroscopic optical behavior within the material, and how covalent bonds and non-covalent interactions, such as hydrogen bonds, determine refractive indices and birefringence. Particular attention is devoted to the peptide bonds as they provide links to build biomacromolecules or polymers. An adequate quantum-mechanical treatment of at least the first interaction sphere of a given functional group is required to properly describe the effects of mutual polarization, but we identified optimum cluster size and shape to better estimate polarizabilities and dipole moments of larger molecules or molecular aggregates from the knowledge of the electron density of a central molecule or amino acid residual that is representative of the bulk. The strategy outlined here is a fast yet effective tool for estimating the optical properties of proteins but could eventually find application in the rational design of optical organic materials as well. METHODS: Electronic-structure calculations were performed on the Gaussin16 program at the DFT level using the CAMB3LYP functional and the double-ζ quality Dunning basis set aug-cc-pVDZ. Electron density partitioning followed the concepts of the Quantum Theory of Atoms and Molecules (QTAIM) and was performed using the AIMAll program. The locally developed Polaber routine was applied to calculate dipole moment vectors and polarizability tensors. It was amended to include the effects of the local field on a given central molecule by means of a modified Atom-Dipole Interaction Model (ADIM).

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.

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 Field Effects on Atomic and Functional-Group Distributed Polarizabilities of Molecular Materials.

To rationally design new molecular materials with desirable linear optical properties, such as refractive index or birefringence, we investigated how atomic and functional-group polarizability tensors of prototypical molecules respond to crystal field effects. By building finite aggregates of urea, succinic acid, p-nitroaniline, 4-mercaptopyridine, or methylbenzoate, and by partitioning the cluster electronic density using quantum theory of atoms in molecules, we could extract atoms and functional groups from the aggregates and estimate their polarizability enhancements with respect to values calculated for molecules in isolation. The isotropic polarizability and its anisotropy for the molecular building blocks are used to understand the functional-group sources of optical properties in these model systems, which could help the synthetic chemist to fabricate efficient materials. This analysis is complemented by benchmarking density functionals for atomic distributed polarizabilities in gas phase, by comparing the results with refractive-index calculations under periodic boundary conditions, and by estimating functional-group optical properties from a classical electrostatic atom-dipole interaction model.

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.

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

Terminal sulfonic acid groups characterize various proton conducting materials including metal-organic frameworks (MOFs). These groups, however, show strong coordination ability that hinders their direct intact incorporation. We present a strategy for introducing pendant SO3H groups into frameworks from sulfonyl chloride precursors. The strategy using concerted deprotonation-metalation-hydrolysis reaction yields a new MOF capable of proton transport.

Accurate Modelling of Group Electrostatic Potential and Distributed Polarizability in Dipeptides.

Within the scope of accurate structure-property correlations in biomolecules, this work investigates how conformations and electronic configurations of biologically relevant macromolecules affect their intermolecular potentials. With the purpose of testing the suitability of a simple and universal model, the dipeptides are made from the assembly of their building blocks, namely the amino acid residuals or, more finely tuned, the individual functional groups. The model makes use of functional-group electrostatic potentials (GEP) and distributed polarizabilities (GDP), which enable an in depth analysis of the correlation between structural features and property build-up. GEPs and GDPs are calculated for various conformers and protonation states of L-alanyl-L-alanine, glycyl-L-alanine, L-alanylglycine, and glycylglycine, which are prototypic molecules to model the pertinent functional groups. The model provides GEPs that reproduce the exact potential to an average accuracy of ca. 0.05 au. The good agreement between the properties estimated with the simple model and those calculated with state-of-the-art quantum chemical methods encourages further testing of the predictive power of this model, simulating for example interaction energies and optoelectronic properties.

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.