Structural analysis and multipole modelling of quercetin monohydrate – a quantitative and comparative study

Excited-state proton transfer based fluorescence in Kaempferol powder and solutions with different concentrations

Kaempferol (KMP) is one of the most common flavonoids, currently being extensively studied for its numerous beneficial health effects. Here we study the fluorescence (FL) emission of KMP powder and of its solutions prepared using different types of solvents (polar and non-polar). In the spectra of KMP powder and KMP solutions with high concentration, the same FL peak with maximum at 1.9 eV is observed. Another FL peak, at higher energy of 2.45 eV, emerges in solutions, its relative intensity increases with decreasing solution concentration. The FL emission of solutions with lowest concentration displays only that peak. To calculate characteristic energies of absorption and emission of KMP molecule in vacuum and in solutions we use time-dependent density functional theory. Comparing the results of computations with measured FL spectra, we associate the FL band at 1.9 eV with the emission due to excited state intramolecular transfer of the proton of -OH5 hydroxyl group. The FL emission at 2.45 eV is related to the -OH3 proton transfer. We measure the FL spectra of KMP powder using two different excitation energies, 3.06 eV and 2.33 eV, and find that its FL spectrum depends on the excitation energy. To understand that dependence, we compare the FL spectra of KMP and Q monohydrate powders. We consider the excited state intermolecular transfer of the proton from -OH3' hydroxyl group to a neighboring molecule in Q crystal and calculate the energy corresponding to the emission of the resulted anion of Q molecule. The spectral feature at 1.69 eV observed only in the FL spectrum of Q hydrate is attributed to the Q anion FL emission.

Molecular Insights into Water-Chloride and Water-Water Interactions in the Supramolecular Architecture of Aconine Hydrochloride Dihydrate

Despite the previous preparation of aconine hydrochloride monohydrate (AHM), accurate determination of the crystal's composition was hindered by severely disordered water molecules within the crystal. In this study, we successfully prepared a new dihydrate form of the aconine hydrochloride [C25H42NO9+Cl-·2(H2O), aconine hydrochloride dihydrate (AHD)] and accurately refined all water molecules within the AHD crystal. Our objective is to elucidate both water-chloride and water-water interactions in the AHD crystal. The crystal structure of AHD was determined at 136 K using X-ray diffraction and a multipolar atom model was constructed by transferring charge-density parameters to explore the topological features of key short contacts. By comparing the crystal structures of dihydrate and monohydrate forms, we have observed that both AHD and AHM exhibit identical aconine cations, except for variations in the number of water molecules present. In the AHD crystal, chloride anions and water molecules serve as pivotal connecting hubs to establish three-dimensional hydrogen bonding networks and one-dimensional hydrogen bonding chain; both water-chloride and water-water interactions assemble supramolecular architectures. The crystal packing of AHD exhibits a complete reversal in the stacking order compared to AHM, thereby emphasizing distinct disparities between them. Hirshfeld surface analysis reveals that H···Cl- and H···O contacts play a significant role in constructing the hydrogen bonding network and chain within these supramolecular architectures. Furthermore, topological analysis and electrostatic interaction energy confirm that both water-chloride and water-water interactions stabilize supramolecular architectures through electrostatic attraction facilitated by H···Cl- and H···O contacts. Importantly, these findings are strongly supported by the existing literature evidence. Consequently, navigating these water-chloride and water-water interactions is imperative for ensuring storage and safe processing of this pharmaceutical compound.

Structural and Anticancer Studies of Methoxyflavone Derivative from Strychnos pseudoquina A.St.-Hil. (Loganiaceae) from Brazilian Cerrado

The Cerrado biome is the world's largest and most diversified tropical savanna. Despite its diversity, there remains a paucity of scientific discussion and evidence about the medicinal use of Cerrado plants. One of the greatest challenges is the complexity of secondary metabolites, such as flavonoids, present in those plants and their extraction, purification, and characterization, which involves a wide range of approaches, tools, and techniques. Notwithstanding these difficulties, the search for accurately proven medicinal plants against cancer, a leading cause of death worldwide, has contributed to this growing area of research. This study set out to extract, purify, and characterize 3-O-methylquercetin isolated from the plant Strychnos pseudoquina A.St.-Hil. (Loganiaceae) and to test it for antiproliferative activity and selectivity against different tumor and nontumor human cell lines. A combined-method approach was employed using 1H and 13C nuclear magnetic resonance, thermogravimetric analysis, differential scanning calorimetry, single-crystal X-ray diffraction, Hirshfeld surface analysis, and theoretical calculations to extensively characterize this bioflavonoid. 3-O-methylquercetin melts around 275 °C and crystallizes in a nonplanar conformation with an angle of 18.02° between the pyran ring (C) and the phenyl ring (B), unlike quercetin and luteolin, which are planar. Finally, the in vitro cytotoxicity of 3-O-methylquercetin was compared with data from quercetin, luteolin, and cisplatin, showing that structural differences influenced the antiproliferative activity and the selectivity against different tumor cell lines.

Navigating the Complex Solid Form Landscape of the Quercetin Flavonoid Molecule

Quercetin, a naturally occurring bioflavonoid substance widely used in the nutraceutical and food industries, exists in various solid forms that can have different physicochemical properties, thus impacting this compound's performance in various applications. In this work, we will clarify the complex solid-form landscape of this molecule. Two elusive isostructural solvates of quercetin were obtained from ethanol and methanol. The obtained crystals were characterized experimentally, but the crystallographic structure could not be solved due to their high instability. Nevertheless, the desolvated structure resulting from a high-temperature treatment (or prolonged storage at ambient conditions) of both these two labile crystals was characterized and solved via powder X-ray diffraction and solid-state nuclear magnetic resonance (SSNMR). This anhydrous crystal structure was compared with another anhydrous quercetin form obtained in our previous work, indicating that, at least, two different anhydrous polymorphs of quercetin exist. Navigating the solid-form landscape of quercetin is essential to ensure accurate control of the functional properties of food, nutraceutical, or pharmaceutical products containing crystal forms of this substance.

The Raman Active Vibrations of Flavone and Quercetin: The Impact of Conformers and Hydrogen Bonding on Fingerprint Modes

The detection and analysis of flavonoids by Raman spectroscopy are of interest in many fields, including medicinal chemistry, food science, and astrobiology. Spectral interpretation would benefit from better identification of the fingerprint vibrational peaks of different flavonoids and how they are affected by intermolecular interactions. The Raman spectra of two flavonoids, flavone and quercetin, were investigated through comparisons between spectra recorded from pure powders and spectra calculated with time dependent density functional theory (TDDFT). For both flavone and quercetin, 17 peaks were assigned to specific molecular vibrations. Both flavonoids were found to have a split peak between 1250-1350 cm^-1 that is not predicted by TDDFT calculations on isolated molecules. In each case, it is shown that the addition of hydrogen bonded molecules arranged based on crystal structures reproduces the split peaks. These peaks were due to a stretching vibration of the bond between benzopyrone and phenyl rings and represent a characteristic spectral feature of flavonoids. Spectra of pollen grains from Quercus virginiana were also recorded and exhibit several peaks that correspond to the quercetin spectrum.

Probing the intermolecular interactions, binding affinity, charge density distribution and dynamics of silibinin in dual targets AChE and BACE1: QTAIM and molecular dynamics perspective

Alzheimer's disease (AD) is the grievous neurodegenerative disorder. Reportedly, many enzymes are responsible for this disease, in which notably, acetylcholinesterase (AChE) and β-secretase (BACE1) are largely involved for AD. An experimental study reports that silibinin molecule inhibits both AChE and BACE1 enzymes. Present study aims to understand the dual binding mechanism of silibinin in the active site of AChE and BACE1 from the intermolecular interactions, conformational flexibility, charge density distribution, binding energy and the stability of molecule. To obtain the above information, the molecular docking, molecular dynamics (MD) and QTAIM (quantum theory of atoms in molecules) calculations have been performed. The molecular docking reveals that silibinin molecule is forming strong and weak intermolecular interactions with the catalytic site of both enzymes. The QTAIM analysis for the binding pockets of both complexes shows the charge density distribution of intermolecular interactions. The electrostatic potential map displays the electronegative/positive regions at the interaction zone of silibinin with AChE and BACE1 complexes. The MD simulation confirms that the silibinin molecule is stable in the active site of AChE and BACE1 enzymes. The binding free energies of silibinin with both enzymes are more favorable to have the interactions.Communicated by Ramaswamy H. Sarma.

Relating Crystal Structure to Surface Properties: A Study on Quercetin Solid Forms

The surface energy and surface chemistry of a crystal are of great importance when designing particles for a specific application, as these will impact both downstream manufacturing processes as well as final product quality. In this work, the surface properties of two different quercetin solvates (quercetin dihydrate and quercetin DMSO solvate) were studied using molecular (synthonic) modeling and experimental techniques, including inverse gas chromatography (IGC) and contact angle measurements, to establish a relationship between crystal structure and surface properties. The attachment energy model was used to predict morphologies and calculate surface properties through the study of their growth synthons. The modeling results confirmed the surface chemistry anisotropy for the two forms. For quercetin dihydrate, the {010} facets were found to grow mainly by nonpolar offset quercetin-quercetin stacking interactions, thus being hydrophobic, while the {100} facets were expected to be hydrophilic, growing by a polar quercetin-water hydrogen bond. For QDMSO, the dominant facet {002} grows by a strong polar quercetin-quercetin hydrogen bonding interaction, while the second most dominant facet {011} grows by nonpolar π-π stacking interactions. Water contact angle measurements and IGC confirmed a greater overall surface hydrophilicity for QDMSO compared to QDH and demonstrated surface energy heterogeneity for both structures. This work shows how synthonic modeling can help in the prediction of the surface nature of crystalline particles and guide the choice of parameters that will determine the optimal crystal form and final morphology for targeted surface properties, for example, the choice of crystallization conditions, choice of solvent, or presence of additives or impurities, which can direct the crystallization of a specific crystal form or crystal shape.

Influence of catecholic ring torsion on hydroxyflavones

Systematic quantum chemical investigation of quercetin and selected eight mono- and bihydroxyflavonols is presented. Structural analysis based on the Density Functional Theory showed that the energetically preferred conformation of flavonols substituted at the C5 and C3 atoms by a hydroxyl group is stabilised via intramolecular hydrogen bonds occurring between the (C4)O···HO(3 or 5) atomic pairs. Depending on the hydroxyl group positions, energetically preferred torsional orientation of the phenyl ring with respect to the planar benzo-γ-pyrone moiety changed from 0 to 180 degrees. Gas-phase electron transitions were investigated using the time-dependent DFT treatment. The dependence of maximal wavelengths on the torsional deformation of the phenyl ring is of a similar shape, i.e. minima observed for the perpendicular orientation and maxima for the planar one. Shape and energies of the Highest Occupied (HOMO) and Lowest Unoccupied (LUMO) Molecular Orbitals were compared. The obtained theoretical results were compared with available experimental data.

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X-H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X-H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d_min ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

A Hidden Side of the Conformational Mobility of the Quercetin Molecule Caused by the Rotations of the O3H, O5H and O7H Hydroxyl Groups: In Silico Scrupulous Study

In this study at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of quantum-mechanical theory it was explored conformational variety of the isolated quercetin molecule due to the mirror-symmetrical hindered turnings of the O3H, O5H and O7H hydroxyl groups, belonging to the A and C rings, around the exocyclic C–O bonds. These dipole active conformational transformations proceed through the 72 transition states (TSs; C1 point symmetry) with non-orthogonal orientation of the hydroxyl groups relatively the plane of the A or C rings of the molecule (HO7C7C8/HO7C7C6 = ±(89.9–93.3), HO5C5C10 = ±(108.9–114.4) and HO3C3C4 = ±(113.6–118.8 degrees) (here and below signs ‘±’ corresponds to the enantiomers)) with Gibbs free energy barrier of activation ΔΔGTS in the range 3.51–16.17 kcal·mol−1 under the standard conditions (T = 298.1 K and pressure 1 atm): ΔΔGTSO7H (3.51–4.27) < ΔΔGTSO3H (9.04–11.26) < ΔΔGTSO5H (12.34–16.17 kcal mol−1). Conformational dynamics of the O3H and O5H groups is partially controlled by the intramolecular specific interactions O3H…O4, C2′/C6′H…O3, O3H…C2′/C6′, O5H…O4 and O4…O5, which are flexible and cooperative. Dipole-active interconversions of the enantiomers of the non-planar conformers of the quercetin molecule (C1 point symmetry) is realized via the 24 TSs with C1 point symmetry (HO3C3C2C1 = ±(11.0–19.1), HC2′/C6′C1′C2 = ±(0.6–2.9) and C3C2C1′C2′/C3C2C1′C6′ = ±(1.7–9.1) degree; ΔΔGTS = 1.65–5.59 kcal·mol−1), which are stabilized by the participation of the intramolecular C2′/C6′H…O1 and O3H…HC2′/C6′ H-bonds. Investigated conformational rearrangements are rather quick processes, since the time, which is necessary to acquire thermal equilibrium does not exceed 6.5 ns.

Refinement of organic crystal structures with multipolar electron scattering factors

A revolution in resolution is occurring now in electron microscopy arising from the development of methods for imaging single particles at cryogenic temperatures and obtaining electron diffraction data from nanocrystals of small organic molecules or macromolecules. Near-atomic or even atomic resolution of molecular structures can be achieved. The basis of these methods is the scattering of an electron beam due to the electrostatic potential of the sample. To analyse these high-quality experimental data, it is necessary to use appropriate atomic scattering factors. The independent atom model (IAM) is commonly used although various more advanced models, already known from X-ray diffraction, can also be applied to enhance the analysis. In this study a comparison is presented of IAM and TAAM (transferable aspherical atom model), the latter with the parameters of the Hansen-Coppens multipole model transferred from the University at Buffalo Databank (UBDB). By this method, TAAM takes into account the fact that atoms in molecules are partially charged and are not spherical. Structure refinements were performed on a carbamazepine crystal using electron structure-factor amplitudes determined experimentally [Jones et al. (2018). ACS Cent. Sci. 4, 1587-1592] or modelled with theoretical quantum-mechanical methods. The results show the possibilities and limitations of the TAAM method when applied to electron diffraction. Among others, the method clearly improves model fitting statistics, when compared with IAM, and allows for reliable refinement of atomic thermal parameters. The improvements are more pronounced with poorer-resolution diffraction data.

Electron density learning of non-covalent systems

Chemists continuously harvest the power of non-covalent interactions to control phenomena in both the micro- and macroscopic worlds. From the quantum chemical perspective, the strategies essentially rely upon an in-depth understanding of the physical origin of these interactions, the quantification of their magnitude and their visualization in real-space. The total electron density ρ( r ) represents the simplest yet most comprehensive piece of information available for fully characterizing bonding patterns and non-covalent interactions. The charge density of a molecule can be computed by solving the Schrödinger equation, but this approach becomes rapidly demanding if the electron density has to be evaluated for thousands of different molecules or very large chemical systems, such as peptides and proteins. Here we present a transferable and scalable machine-learning model capable of predicting the total electron density directly from the atomic coordinates. The regression model is used to access qualitative and quantitative insights beyond the underlying ρ( r ) in a diverse ensemble of sidechain-sidechain dimers extracted from the BioFragment database (BFDb). The transferability of the model to more complex chemical systems is demonstrated by predicting and analyzing the electron density of a collection of 8 polypeptides.

Polarization of Electron Density Databases of Transferable Multipolar Atoms

Polarizability is a key molecular property involved in either macroscopic (i.e., dielectric constant) and microscopic properties (i.e., interaction energies). In rigid molecules, this property only depends on the ability of the electron density (ED) to acquire electrostatic moments in response to applied electric fields. Databases of transferable electron density fragments are a cheap and efficient way to access molecular EDs. This approach is rooted in the relative conservation of the atomic ED between different molecules, termed transferability principle. The present work discusses the application of this transferability principle to the polarizability, an electron density-derived property, partitioned in atomic contributions using the Quantum Theory of Atoms In Molecules topology. The energetic consequences of accounting for in situ deformation (polarization) of database multipolar atoms are investigated in detail by using a high-quality quantum chemical benchmark.

Transferable Machine-Learning Model of the Electron Density

The electronic charge density plays a central role in determining the behavior of matter at the atomic scale, but its computational evaluation requires demanding electronic-structure calculations. We introduce an atom-centered, symmetry-adapted framework to machine-learn the valence charge density based on a small number of reference calculations. The model is highly transferable, meaning it can be trained on electronic-structure data of small molecules and used to predict the charge density of larger compounds with low, linear-scaling cost. Applications are shown for various hydrocarbon molecules of increasing complexity and flexibility, and demonstrate the accuracy of the model when predicting the density on octane and octatetraene after training exclusively on butane and butadiene. This transferable, data-driven model can be used to interpret experiments, accelerate electronic structure calculations, and compute electrostatic interactions in molecules and condensed-phase systems.

Intermolecular head-to-head interaction of carbonyl groups in bicyclic hydrogen-bonded synthon based on β-hydroxy ketones

In this study, we report a counterintuitive carbonyl–carbonyl interaction explored for crystalline (2RS,3RS)-1-aryl-2-bromo-3-hydroxy-3-(2-nitrophenyl)-propan-1-ones.

Libraries of Extremely Localized Molecular Orbitals. 3. Construction and Preliminary Assessment of the New Databanks

The fast and reliable determination of wave functions and electron densities of macromolecules has been one of the goals of theoretical chemistry for a long time, and in this context, several linear scaling techniques have been successfully devised over the years. Different approaches have been adopted to tackle this problem, and one of them exploits the fact that, according to the traditional chemical perception, molecules can be seen as constituted of recurring units (e.g., functional groups) with well-defined chemical features. This has led to the development of methods in which the global wave functions or electron densities of macromolecules are obtained by simply transferring density matrices or fuzzy electron densities associated with molecular fragments. In this context, we propose an alternative strategy that aims at quickly reconstructing wave functions and electron densities of proteins through the transfer of extremely localized molecular orbitals (ELMOs), which are orbitals strictly localized on small molecular units and, for this reason, easily transferable from molecule to molecule. To accomplish this task we have constructed original libraries of ELMOs that cover all the possible elementary fragments of the 20 natural amino acids in all their possible protonation states and forms. Our preliminary test calculations have shown that, compared to more traditional methods of quantum chemistry, the transfers from the novel ELMO databanks allow to obtain wave function and electron densities of large polypeptides and proteins at a significantly reduced computational cost. Furthermore, notwithstanding expected discrepancies, the obtained electron distributions and electrostatic potentials are in very good agreement with those obtained at Hartree-Fock and density functional theory (DFT) levels. Therefore, the results encourage to use the new libraries as alternatives to the popular pseudoatom-databases of crystallography in the refinement of crystallographic structures of macromolecules. In particular, in this context, we have already envisaged the coupling of the ELMO databanks with the promising Hirshfeld atom refinement technique to extend the applicability of the latter to very large systems.

Infrared spectroscopy of flavones and flavonols. Reexamination of the hydroxyl and carbonyl vibrations in relation to the interactions of flavonoids with membrane lipids

Detailed vibrational assignments for twelve flavonoids (seven flavones (flavone, 3- and 5-hydroxyflavone, chrysin, apigenin, fisetin and luteolin) and five flavonols (galangin, kaempferol, quercetin, morin and myricetin)) have been made based on own and reported experimental data and calculations at the B3LYP/6-31+G(d,p) level of theory. All the molecules are treated in a uniform way by using the same set of redundancy-free set of internal coordinates. A generalized harmonic mode mixing is used to corroborate the vibrational characteristics of this important class of molecules. Each flavonoid molecule can be treated from the vibrational point of view as made of relatively weakly coupled chromone and phenyl part. It has been shown that the strongest band around 1600cm^-1 need not be attributable to the CO stretching. The way the vibrations of any of the hydroxyl groups are mixed with ring vibrations and vibrations of other neighboring hydroxyl groups is rather involved. This imposes severe limitations on any attempt to describe normal modes of a flavonol in terms of hydroxyl or carbonyl group vibrations. The role of water molecules in the appearance of flavonoid IR spectra is emphasized. Knowing for the great affinity of phosphate groups in lipids towards water, the immediate consequence is a reasonable assumption that flavonoid lipid interactions is mediated by water.

Dietary quercetin potentiates the antiproliferative effect of interferon-α in hepatocellular carcinoma cells through activation of JAK/STAT pathway signaling by inhibition of SHP2 phosphatase

Type I interferons (IFN-α/β) have broad and potent immunoregulatory and antiproliferative activities, which are negatively regulated by Src homology domain 2 containing tyrosine phosphatase-2 (SHP-2). Inhibition of SHP2 by small molecules may be a new strategy to enhance the effcacy of type I IFNs. Using an in vitro screening assay for new inhibitors of SHP2 phosphatase, we found that quercetin was a potent inhibitor of SHP2. Computational modeling showed that quercetin exhibited an orientation favorable to nucleophilic attack in the phosphatase domain of SHP2. Quercetin enhanced the phosphorylation of signal transducer and activator of transcription proteins 1 (STAT1) and promoted endogenous IFN-α-regulated gene expression. Furthermore, quercetin also sensitized the antiproliferative effect of IFN-α on hepatocellular carcinoma HepG2 and Huh7 cells. The overexpression of SHP2 attenuated the effect of quercetin on IFN-α-stimulated STAT1 phosphorylation and antiproliferative effect, whereas the inhibition of SHP2 promoted the effect of quercetin on IFN-α-induced STAT1 phosphorylation and antiproliferative effect. The results suggested that quercetin potentiated the inhibitory effect of IFN-α on cancer cell proliferation through activation of JAK/STAT pathway signaling by inhibiting SHP2. Quercetin warrants further investigation as a novel therapeutic method to enhance the efficacy of IFN-α/β.

A theoretical-electron-density databank using a model of real and virtual spherical atoms

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

Transferred multipolar atom model for 10β,17β-dihydroxy-17α-methylestr-4-en-3-one dihydrate obtained from the biotransformation of methyloestrenolone

Biotransformation is the structural modification of compounds using enzymes as the catalysts and it plays a key role in the synthesis of pharmaceutically important compounds. 10β,17β-Dihydroxy-17α-methylestr-4-en-3-one dihydrate, C19H28O3·2H2O, was obtained from the fungal biotransformation of methyloestrenolone. The structure was refined using the classical independent atom model (IAM) and a transferred multipolar atom model using the ELMAM2 database. The results from the two refinements have been compared. The ELMAM2 refinement has been found to be superior in terms of the refinement statistics. It has been shown that certain electron-density-derived properties can be calculated on the basis of the transferred parameters for crystals which diffract to ordinary resolution.

Highly sensitive solid forms discrimination on the whole tablet of the active ingredients in quercetin dietary supplements by NMR crystallography approaches

Similarly to synthetic drugs, the exact crystalline form of active ingredients in solid formulations of dietary supplements may directly influence the dissolution rate, bioavailability, and stability of the final product, but this information is usually not provided by manufacturers. Working on the examples of two commercial quercetin dietary supplements a quick, reliable, and sensitive method is introduced for quercetin solid forms discrimination directly on the marketed products, without the need for prior sample preparation. It exploits the complementarity between solid-state Nuclear Magnetic Resonance (ss-NMR) and Powder X-Ray Diffraction (PXRD), which proved essential for performing a complete and accurate solid-state characterization of the two commercial products, and for obtaining new insights into the complex quercetin solid-forms landscape. The method can be readily generalized also to other dietary supplements based on bio-flavonoids/polyphenols.

Libraries of Extremely Localized Molecular Orbitals. 2. Comparison with the Pseudoatoms Transferability

Due to both technical and methodological difficulties, determining and analyzing charge densities of very large molecular systems represents a serious challenge that, in the crystallographers community, has been mainly tackled by observing that the so-called pseudoatoms of the electron density multipole expansions are reliably transferable from molecule to molecule. This has led to the construction of pseudoatoms databanks that have allowed successful refinements of crystallographic structures of macromolecules, while taking into account their corresponding reconstructed electron distributions. A recent alternative/complement to the previous approach is represented by techniques based on extremely localized molecular orbitals (ELMOs) that, due to their strict localization on small molecular fragments (e.g., atoms, bonds, and functional groups), are also in principle exportable from system to system. The ELMOs transferability has been already tested in detail, and, in this work, it has been compared to the one of the pseudoatoms. To accomplish this task, electron distributions obtained both through the transfer of pseudoatoms and through the transfer of extremely localized molecular orbitals have been analyzed, especially taking into account topological properties and similarity indexes. The obtained results indicate that all the considered reconstruction methods give completely reasonable and similar charge densities, and, consequently, the new ELMOs libraries will probably represent new useful tools not only for refining crystal structures but also for computing approximate electronic properties of very large molecules.

Modelling the experimental electron density: only the synergy of various approaches can tackle the new challenges

Electron density is a fundamental quantity that enables understanding of the chemical bonding in a molecule or in a solid and the chemical/physical property of a material. Because electrons have a charge and a spin, two kinds of electron densities are available. Moreover, because electron distribution can be described in momentum or in position space, charge and spin density have two definitions and they can be observed through Bragg (for the position space) or Compton (for the momentum space) diffraction experiments, using X-rays (charge density) or polarized neutrons (spin density). In recent years, we have witnessed many advances in this field, stimulated by the increased power of experimental techniques. However, an accurate modelling is still necessary to determine the desired functions from the acquired data. The improved accuracy of measurements and the possibility to combine information from different experimental techniques require even more flexibility of the models. In this short review, we analyse some of the most important topics that have emerged in the recent literature, especially the most thought-provoking at the recent IUCr general meeting in Montreal.

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

Can the conformation of flexible hydroxyl groups be constrained by simple NMR crystallography approaches? The case of the quercetin solid forms

Hydrogen atoms in systems with many flexible hydroxyl side-groups are difficult to be exactly located from experimental X-Ray diffraction and/or solid-state NMR data, thus often leading to wrong conclusions with respect to the hydrogen bonding network established in crystal lattice. A simple computational method is proposed in the present work to tackle this problem, which may be readily incorporated in conventional NMR crystallography protocols. The method is based on ranking all possible conformations of the flexible hydroxyls according to their lattice energy in crystalline environments. Its effectiveness is investigated on two distinct solid forms of quercetin, for which only two out of the five hydroxyl side-groups can be well constrained from experimental/theoretical data. For this purpose, first-principle quantum-mechanical computations were combined with calculations at the molecular mechanics (MM) level of theory, and previous ss-NMR and X-Ray diffraction data. To assess accuracy in ranking the identified conformers, tests have been performed first on quercetin dihydrate, for which an X-Ray single-crystal structure is available. The possibility of applying this method in a real NMR crystallography context has been investigated finally on anhydrous quercetin, for which only powder X-Ray crystal structure has been reported so far.

Properties and applications of flavonoid metal complexes

Flavonoid metal complexes have a wide spectrum of activities as well as potential and actual applications.

Isomorphism and solid solution as shown by an accurate high-resolution diffraction experiment

High-resolution crystal structure determination and spherical and multipolar refinement enabled an organic solid solution of 1-(4'-chlorophenyl)-2-methyl-4-nitro-1H-imidazole-5-carbonitrile and 5-bromo-1-(4'-chlorophenyl)-2-methyl-4-nitro-1H-imidazole to be found, which would not normally be revealed using only standard resolution data (ca 0.8 Å), as the disordered part is only visible at high resolution. Therefore, this new structure would have been reported as just another polymorphic form, even more reasonably as isostructural with other derivatives. To the best of our knowledge this is the first example of organic solid solution modelled via charge density Hansen-Coppens formalism and analysed by means of quantum theory of atoms in molecules (QTAIM) theory.

1H-NMR as a structural and analytical tool of intra- and intermolecular hydrogen bonds of phenol-containing natural products and model compounds

Experimental parameters that influence the resolution of 1H-NMR phenol OH signals are critically evaluated with emphasis on the effects of pH, temperature and nature of the solvents. Extremely sharp peaks (Δν1/2≤2 Hz) can be obtained under optimized experimental conditions which allow the application of 1H-13C HMBC-NMR experiments to reveal long range coupling constants of hydroxyl protons and, thus, to provide unequivocal assignment of the OH signals even in cases of complex polyphenol natural products. Intramolecular and intermolecular hydrogen bonds have a very significant effect on 1H OH chemical shifts which cover a region from 4.5 up to 19 ppm. Solvent effects on -OH proton chemical shifts, temperature coefficients (Δδ/ΔT), OH diffusion coefficients, and nJ(13C, O1H) coupling constants are evaluated as indicators of hydrogen bonding and solvation state of phenol -OH groups. Accurate 1H chemical shifts of the OH groups can be calculated using a combination of DFT and discrete solute-solvent hydrogen bond interaction at relatively inexpensive levels of theory, namely, DFT/B3LYP/6-311++G (2d,p). Excellent correlations between experimental 1H chemical shifts and those calculated at the ab initio level can provide a method of primary interest in order to obtain structural and conformational description of solute-solvent interactions at a molecular level. The use of the high resolution phenol hydroxyl group 1H-NMR spectral region provides a general method for the analysis of complex plant extracts without the need for the isolation of the individual components.

Investigation of solute-solvent interactions in phenol compounds: accurate ab initio calculations of solvent effects on 1H NMR chemical shifts

Accurate (1)H chemical shifts of the -OH groups of polyphenol compounds can be calculated, compared to experimental values, using a combination of DFT, polarizable continuum model (PCM) and discrete solute-solvent hydrogen bond interactions. The study focuses on three molecular solutes: phenol, 4-methylcatechol and the natural product genkwanin in DMSO, acetone, acetonitrile, and chloroform. Excellent linear correlation between experimental and computed chemical shifts (with the GIAO method at the DFT/B3LYP/6-311++G(2d,p) level) was obtained with minimization of the solvation complexes at the DFT/B3LYP/6-31+G(d) and DFT/B3LYP/6-311++G(d,p) level of theory with a correlation coefficient of 0.991. The use of the DFT/B3LYP/6-31+G(d) level of theory for minimization could provide an excellent means for the accurate prediction of the experimental OH chemical shift range of over 8 ppm due to: (i) strong intramolecular and solute-solvent intermolecular hydrogen bonds, (ii) flip-flop intramolecular hydrogen bonds, and (iii) conformational effects of substituents of genkwanin. The combined use of ab initio calculations and experimental (1)H chemical shifts of phenol -OH groups provides a method of primary interest in order to obtain detailed structural, conformation and electronic description of solute-solvent interactions at a molecular level.

About systematic errors in charge-density studies

The formerly introduced theoretical R values [Henn & Schönleber (2013). Acta Cryst. A69, 549-558] are used to develop a relative indicator of systematic errors in model refinements, R(meta), and applied to published charge-density data. The counter of R(meta) gives an absolute measure of systematic errors in percentage points. The residuals (Io - Ic)/σ(Io) of published data are examined. It is found that most published models correspond to residual distributions that are not consistent with the assumption of a Gaussian distribution. The consistency with a Gaussian distribution, however, is important, as the model parameter estimates and their standard uncertainties from a least-squares procedure are valid only under this assumption. The effect of correlations introduced by the structure model is briefly discussed with the help of artificial data and discarded as a source of serious correlations in the examined example. Intensity and significance cutoffs applied in the refinement procedure are found to be mechanisms preventing residual distributions from becoming Gaussian. Model refinements against artificial data yield zero or close-to-zero values for R(meta) when the data are not truncated and small negative values in the case of application of a moderate cutoff Io > 0. It is well known from the literature that the application of cutoff values leads to model bias [Hirshfeld & Rabinovich (1973). Acta Cryst. A29, 510-513].

Mid-infrared spectroscopy as a polymer selection tool for formulating amorphous solid dispersions

Objectives

The development of amorphous solid dispersions is of increasing interest in the delivery of bioactive compounds; however, there is a need for a methodology that enables the rational selection of polymers for solid dispersion formulations with optimal stability to crystallization. The objective of this study was to evaluate the use of mid-infrared (IR) spectroscopy for this purpose.

Methods

Polymers evaluated included poly(vinylpyrrolidone) (PVP), Eudragit E100 (E100), carboxymethylcellulose acetate butyrate (CMCAB), hydroxypropylmethylcellulose (HPMC), HPMC acetate succinate (HPMCAS) and poly(acrylic acid) (PAA). Model crystalline bioactive polyphenols included quercetin and naringenin. Amorphous solid dispersions were prepared by dissolving both polyphenol and polymer in a common solvent followed by solvent evaporation. Mid-IR spectroscopy was used to determine and quantify the extent of polyphenol–polymer interactions, and powder X-ray diffraction was used to monitor physical stability following storage at different environmental conditions.

Key findings

The mid-IR analysis suggested the following rank order for the crystallization-inhibiting performance of the different polymers: E100 &gt; PVP &gt; HPMCAS &gt; HPMC ≥ CMCAB &gt; PAA. The initial performance of the different polymers was evaluated using the highest concentration of polyphenol for which x-ray amorphous solid dispersions could be prepared via rotary evaporation. The observed stability followed that predicted from the mid-infrared spectroscopy evaluation of intermolecular interactions. The dispersions with better polyphenol–polymer interactions were stable against crystallization when exposed to high relative humidity and high temperatures; on the other hand, systems that had weak interactions were not stable to crystallization when stored at moderate environmental conditions.

Conclusions

Based on the observed ability of mid-IR analysis to enable the characterization of intermolecular polyphenol–polymer interactions and based on the correlation between the extent of intermolecular interactions and the crystallization-inhibiting performance of polymers, it can be concluded that this technique is an important tool for the rational formulation of solid dispersions with optimized physical stability.

Experimental and database-transferred electron-density analysis and evaluation of electrostatic forces in coumarin-102 dye

The electron-density distribution of a new crystal form of coumarin-102, a laser dye, has been investigated using the Hansen-Coppens multipolar atom model. The charge density was refined versus high-resolution X-ray diffraction data collected at 100 K and was also constructed by transferring the charge density from the Experimental Library of Multipolar Atom Model (ELMAM2). The topology of the refined charge density has been analysed within the Bader `Atoms In Molecules' theory framework. Deformation electron-density peak heights and topological features indicate that the chromen-2-one ring system has a delocalized π-electron cloud in resonance with the N (amino) atom. The molecular electrostatic potential was estimated from both experimental and transferred multipolar models; it reveals an asymmetric character of the charge distribution across the molecule. This polarization effect is due to a substantial charge delocalization within the molecule. The molecular dipole moments derived from the experimental and transferred multipolar models are also compared with the liquid and gas-phase dipole moments. The substantial molecular dipole moment enhancements observed in the crystal environment originate from the crystal field and from intermolecular charge transfer induced and controlled by C-H···O and C-H···N intermolecular hydrogen bonds. The atomic forces were integrated over the atomic basins and compared for the two electron-density models.