Bond lengths in organic and metal-organic compounds revisited: X-H bond lengths from neutron diffraction data

On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors

This study examines various methods for modelling the electron density and, thus, the electrostatic potential of an organometallic complex for use in crystal structure refinement against 3D electron diffraction (ED) data. It focuses on modelling the scattering factors of iron(III), considering the electron density distribution specific for coordination with organic linkers. We refined the structural model of the metal-organic complex, iron(III) acetylacetonate (FeAcAc), using both the independent atom model (IAM) and the transferable aspherical atom model (TAAM). TAAM refinement initially employed multipolar parameters from the MATTS databank for acetylacetonate, while iron was modelled with a spherical and neutral approach (TAAM ligand). Later, custom-made TAAM scattering factors for Fe-O coordination were derived from DFT calculations [TAAM-ligand-Fe(III)]. Our findings show that, in this compound, the TAAM scattering factor corresponding to Fe3+ has a lower scattering amplitude than the Fe3+ charged scattering factor described by IAM. When using scattering factors corresponding to the oxidation state of iron, IAM inaccurately represents electrostatic potential maps and overestimates the scattering potential of the iron. In addition, TAAM significantly improved the fitting of the model to the data, shown by improved R1 values, goodness-of-fit (GooF) and reduced noise in the Fourier difference map (based on the residual distribution analysis). For 3D ED, R1 values improved from 19.36% (IAM) to 17.44% (TAAM-ligand) and 17.49% (TAAM-ligand-Fe3+), and for single-crystal X-ray diffraction (SCXRD) from 3.82 to 2.03% and 1.98%, respectively. For 3D ED, the most significant R1 reductions occurred in the low-resolution region (8.65-2.00 Å), dropping from 20.19% (IAM) to 14.67% and 14.89% for TAAM-ligand and TAAM-ligand-Fe(III), respectively, with less improvement in high-resolution ranges (2.00-0.85 Å). This indicates that the major enhancements are due to better scattering modelling in low-resolution zones. Furthermore, when using TAAM instead of IAM, there was a noticeable improvement in the shape of the thermal ellipsoids, which more closely resembled those of an SCXRD-refined model. This study demonstrates the applicability of more sophisticated scattering factors to improve the refinement of metal-organic complexes against 3D ED data, suggesting the need for more accurate modelling methods and highlighting the potential of TAAM in examining the charge distribution of large molecular structures using 3D ED.

Hirshfeld atom refinement and dynamical refinement of hexagonal ice structure from electron diffraction data

Reaching beyond the commonly used spherical atomic electron density model allows one to greatly improve the accuracy of hydrogen atom structural parameters derived from X-ray data. However, the effects of atomic asphericity are less explored for electron diffraction data. In this work, Hirshfeld atom refinement (HAR), a method that uses an accurate description of electron density by quantum mechanical calculation for a system of interest, was applied for the first time to the kinematical refinement of electron diffraction data. This approach was applied here to derive the structure of ordinary hexagonal ice (Ih). The effect of introducing HAR is much less noticeable than in the case of X-ray refinement and it is largely overshadowed by dynamical scattering effects. It led to only a slight change in the O-H bond lengths (shortening by 0.01 Å) compared with the independent atom model (IAM). The average absolute differences in O-H bond lengths between the kinematical refinements and the reference neutron structure were much larger: 0.044 for IAM and 0.046 Å for HAR. The refinement results changed considerably when dynamical scattering effects were modelled - with extinction correction or with dynamical refinement. The latter led to an improvement of the O-H bond length accuracy to 0.021 Å on average (with IAM refinement). Though there is a potential for deriving more accurate structures using HAR for electron diffraction, modelling of dynamical scattering effects seems to be a necessary step to achieve this. However, at present there is no software to support both HAR and dynamical refinement.

Synthesis, non-spherical structure refinement and Hirshfeld surface analysis of racemic 2,2'-diisobut-oxy-1,1'-bi-naphthalene

In the racemic title compound, C28H30O2, the naphthyl ring systems subtend a dihedral angle of 68.59 (1)° and the mol-ecular conformation is consolidated by a pair of intra-molecular C-H⋯π contacts. The crystal packing features a weak C-H⋯π contact and van der Waals forces. A Hirshfeld surface analysis of the crystal structure reveals that the most significant contributions are from H⋯H (73.2%) and C⋯H/H⋯C (21.2%) contacts.

Catalyzed syntheses of novel series of spiro thiazolidinone derivatives with nano Fe2O3: spectroscopic, X-ray, Hirshfeld surface, DFT, biological and docking evaluations

Twelve spiro thiazolidinone compounds (A-L) were synthesized via either conventional thermal or ultrasonication techniques using Fe2O3 nanoparticles. The modification of the traditional procedure by using Fe2O3 nanoparticles led to enhancement of the yield of the desired candidates to 78-93% in approximately half reaction time compared with 58-79% without catalyst. The products were fully characterized using different analytical and spectroscopic techniques. The structure of the two derivatives 4-phenyl-1-thia-4-azaspirodecan-3-one (A) and 4-(p-tolyl)-1-thia-4-azaspirodecan-3-one (B) were also determined using single crystal X-ray diffraction and Hirshfeld surface analysis. The two compounds (A and B) were crystallized in the orthorhombic system with Pbca and P212121 space groups, respectively. In addition, the crystal packing of compounds revealed the formation of supramolecular array with a net of intermolecular hydrogen bonding interactions. The energy optimized geometries of some selected derivatives were performed by density functional theory (DFT/B3LYP). The reactivity descriptors were also calculated and correlated with their biological properties. All the reported compounds were screened for antimicrobial inhibitions. The two derivatives, F and J, exhibited the highest levels of bacterial inhibition with an inhibition zone of 10-17 mm. Also, the two derivatives, F and J, displayed the most potent fungal inhibition with an inhibition zone of 15-23 mm. Molecular docking investigations of some selected derivatives were performed using a B-DNA (PDB: 1BNA) as a macromolecular target. Structure and activity relationship of the reported compounds were correlated with the data of antimicrobial activities and the computed reactivity parameters.

Intermolecular Metal-Involving Pnictogen Bonding: The Case of σ-(SbIII)-Hole···dz2[PtII] Interaction

Cocrystallizations of trans-[PtX'2(NCNR2)2] (R2 = Me2, X' = Cl 1a, Br 1b, I 1c; R2 = (CH2)5, X' = I 2c) with SbX3 (X = Cl, Br, I) gave 1:2 cocrystals 1a·2SbCl3, 1b·2SbBr3, 1c·2SbCl3, 1c·2SbBr3, 1c·2SbI3, and 2c·2SbI3. In all six X-ray structures, the association of the molecular coformers is achieved mainly by SbIII···dz2[PtII] metal-involving intermolecular pnictogen bonding. Density functional theory (DFT) calculations (based on experimentally determined geometries) using both gas-phase and solid-state approximations revealed that a σ-(Sb)-hole interacts with an area of negative potential associated with the dz2-orbital of the positively charged platinum(II) sites, thus forming a pnictogen bond whose energy falls in the range between -7.3 and -16.9 kcal/mol.

3-[(Benzo-1,3-dioxol-5-yl)amino]-4-methoxycyclobut-3-ene-1,2-dione: polymorphism and twinning of a precursor to an antimycobacterial squaramide

The title compound, 3-[(benzo-1,3-dioxol-5-yl)amino]-4-methoxycyclobut-3-ene-1,2-dione, C12H9NO5 (3), is a precursor to an antimycobacterial squaramide. Block-shaped crystals of a monoclinic form (3-I, space group P21/c, Z = 8, Z' = 2) and needle-shaped crystals of a triclinic form (3-II, space group P-1, Z = 4, Z' = 2) were found to crystallize concomitantly. In both crystal forms, R22(10) dimers assemble through N-H...O=C hydrogen bonds. These dimers are formed from crystallographically unique molecules in 3-I, but exhibit crystallographic Ci symmetry in 3-II. Twinning by pseudomerohedry was encountered in the crystals of 3-II. The conformations of 3 in the solid forms 3-I and 3-II are different from one another but are similar for the unique molecules in each polymorph. Density functional theory (DFT) calculations on the free molecule of 3 indicate that a nearly planar conformation is preferred.

Phase Transition Control in Molecular Solids via Complementarity of Hydrogen-Bond Strength

Phase transitions in molecular solids involve synergistic changes in chemical and electronic structures, leading to diversification in physical and chemical properties. Despite the pivotal role of hydrogen bonds (H-bonds) in many phase-transition materials, it is rare and challenging to chemically regulate the dynamics and to elucidate the structure-property relationship. Here, four high-spin CoII compounds were isolated and systematically investigated by modifying the ligand terminal groups (X=S, Se) and substituents (Y=Cl, Br). S-Cl and Se-Br undergo a reversible structural phase transition near room temperature, triggering the rotation of 15-crown-5 guests and the swing between syn- and anti-conformation of NCX- ligands, accompanied by switchable magnetism. Conversely, S-Br and Se-Cl retain stability in ordered and disordered phases, respectively. H-bonds geometric analysis and ab initio calculations reveal that the electronegativity of X and Y affects the strength of NY-ap-H⋅⋅⋅X interactions. Entropy-driven structural phase transitions occur when the H-bond strength is appropriate; otherwise, the phase stays unchanged if it is too strong or weak. This work highlights a phase transition driven by H-bond strength complementarity - pairing strong acceptor with weak donor and vice versa, which offers a straightforward and effective approach for designing phase-transition molecular solids from a chemical perspective.

Variation of Cyclodextrin (CD) Complexation with Biogenic Amine Tyramine: Pseudopolymorphs of β-CD Inclusion vs. α-CD Exclusion, Deep Atomistic Insights

Tyramine (TRM) is a biogenic catecholamine neurotransmitter, which can trigger migraines and hypertension. TRM accumulated in foods is reduced and detected using additive cyclodextrins (CDs) while their association characteristics remain unclear. Here, single-crystal X-ray diffraction and density functional theory (DFT) calculation have been performed, demonstrating the elusive pseudopolymorphs in β-CD inclusion complexes with TRM base/HCl, β-CD·0.5TRM·7.6H2O (1) and β-CD·TRM HCl·4H2O (2) and the rare α-CD·0.5(TRM HCl)·10H2O (3) exclusion complex. Both 1 and 2 share the common inclusion mode with similar TRM structures in the round and elliptical β-CD cavities, belong to the monoclinic space group P21, and have similar herringbone packing structures. Furthermore, 3 differs from 2, as the smaller twofold symmetry-related, round α-CD prefers an exclusion complex with the twofold disordered TRM-H+ sites. In the orthorhombic P21212 lattice, α-CDs are packed in a channel-type structure, where the column-like cavity is occupied by disordered water sites. DFT results indicate that β-CD remains elliptical to suitably accommodate TRM, yielding an energetically favorable inclusion complex, which is significantly contributed by the β-CD deformation, and the inclusion complex of α-CD with the TRM aminoethyl side chain is also energetically favorable compared to the exclusion mode. This study suggests the CD implications for food safety and drug/bioactive formulation and delivery.

Data mining of arsenic-based small molecules geometrics present in Cambridge structural database

Arsenic, ubiquitous in various industrial processes and consumer products, presents both essential functions and considerable toxicity risks, driving extensive research into safer applications. Our investigation, drawing from 7182 arsenic-containing molecules in the Cambridge Structural Database (CSD), outlines their diverse bonding patterns. Notably, 51% of these molecules exhibit cyclic connections, while 49% display acyclic ones. Arsenic forms eight distinct bonding types with other elements, with significant interactions observed, particularly with phenyl rings, O3 and F6 moieties. Top interactions involve carbon, nitrogen, oxygen, fluorine, sulfur, and arsenic itself. We meticulously evaluated average bond lengths under three conditions: without an R-factor cut-off, with R-factor ≤0.075, and with R-factor ≤0.05, supporting the credibility of our results. Comparative analysis with existing literature data enriches our understanding of arsenic's bonding behaviour. Our findings illuminate the structural attributes, molecular coordination, geometry, and bond lengths of arsenic with 68 diverse atoms, enriching our comprehension of arsenic chemistry. These revelations not only offer a pathway for crafting innovative and safer arsenic-based compounds but also foster the evolution of arsenic detoxification mechanisms, tackling pivotal health and environmental challenges linked to arsenic exposure across different contexts.

Evolution of structure and spectroscopic properties of a new 1,3-diacetylpyrene polymorph with temperature and pressure

A new polymorph of 1,3-diacetylpyrene has been obtained from its melt and thoroughly characterized using single-crystal X-ray diffraction, steady-state UV-Vis spectroscopy and periodic density functional theory calculations. Experimental studies covered the temperature range from 90 to 390 K and the pressure range from atmospheric to 4.08 GPa. Optimal sample placement in a diamond anvil cell according to our previously presented methodology ensured over 80% data coverage up to 0.8 Å for a monoclinic sample. Unrestrained Hirshfeld atom refinement of the high-pressure crystal structures was successful and anharmonic behavior of carbonyl oxygen atoms was observed. Unlike the previously characterized polymorph, the structure of 2°AP-β is based on infinite π-stacks of antiparallel 2°AP molecules. 2°AP-β displays piezochromism and piezofluorochromism which are directly related to the variation in interplanar distances within the π-stacking. The importance of weak intermolecular interactions is reflected in the substantial negative thermal expansion coefficient of -55.8 (57) MK-1 in the direction of C-H...O interactions.

TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules

3D electron diffraction (3D ED), or microcrystal electron diffraction (MicroED), has become an alternative technique for determining the high-resolution crystal structures of compounds from sub-micron-sized crystals. Here, we considered L-alanine, α-glycine and urea, which are known to form good-quality crystals, and collected high-resolution 3D ED data on our in-house TEM instrument. In this study, we present a comparison of independent atom model (IAM) and transferable aspherical atom model (TAAM) kinematical refinement against experimental and simulated data. TAAM refinement on both experimental and simulated data clearly improves the model fitting statistics (R factors and residual electrostatic potential) compared to IAM refinement. This shows that TAAM better represents the experimental electrostatic potential of organic crystals than IAM. Furthermore, we compared the geometrical parameters and atomic displacement parameters (ADPs) resulting from the experimental refinements with the simulated refinements, with the periodic density functional theory (DFT) calculations and with published X-ray and neutron crystal structures. The TAAM refinements on the 3D ED data did not improve the accuracy of the bond lengths between the non-H atoms. The experimental 3D ED data provided more accurate H-atom positions than the IAM refinements on the X-ray diffraction data. The IAM refinements against 3D ED data had a tendency to lead to slightly longer X-H bond lengths than TAAM, but the difference was statistically insignificant. Atomic displacement parameters were too large by tens of percent for L-alanine and α-glycine. Most probably, other unmodelled effects were causing this behaviour, such as radiation damage or dynamical scattering.

N,N'-Diaryl-Sulfurdiimides are Strongly Redox Tuned

The synthesis and extensive characterization of nine aryl sulfur diimides (SDIs, Ar-NSN-Ar) are presented with a robust computational and experimental investigation of the fundamental properties of these important members of the thiazyl family of compounds, with particular attention paid to their highly tunable electrochemical behaviour. This is the first work to undertake a systematic comparison of the electrochemical profiles of a coherent series of SDIs to demonstrate and quantify the response of their reduction potentials to substituent electron-donating and -withdrawing properties. This effect is found to be not only exceptionally strong, but also correlates very closely with computed orbital energies. Electron paramagnetic resonance spectroscopy is used to determine the nature, localization, and qualitative lifetimes of the radical anions of SDIs. This work also addresses significant misconceptions about physical properties of SDIs. Experimental data and modern computational methods are employed to provide a resolute answer to the long-standing contention of the solution-state conformations of SDIs, and to correct historical mistakes in the assignment of infrared spectroscopic data. High-quality crystal structures of all SDIs in this work showcase the utility of the recently introduced structural refinement software NoSpherA2, enabling full anisotropic refinement of H-atoms with accurate C-H bond lengths.

Dynamical refinement with multipolar electron scattering factors

Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petříček & Corrêa, (2015). Acta Cryst. A71, 235-244; Palatinus, Corrêa et al. (2015). Acta Cryst. B71, 740-751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza et al. (2020). Acta Cryst. A76, 92-109; Jha et al. (2021). J. Appl. Cryst. 54, 1234-1243]. In this study, we combine dynamical refinement with TAAM for the crystal structure of 1-methyluracil, using data from precession ED. Our results show that this approach improves the residual Fourier electrostatic potential and refinement figures of merit. Furthermore, it leads to systematic changes in the atomic displacement parameters of all atoms and the positions of hydrogen atoms. We found that the refinement results are sensitive to the parameters used in the TAAM modelling process. Though our results show that TAAM offers superior performance compared with IAM in all cases, they also show that TAAM parameters obtained by periodic DFT calculations on the refined structure are superior to the TAAM parameters from the UBDB/MATTS database. It appears that multipolar parameters transferred from the database may not be sufficiently accurate to provide a satisfactory description of all details of the electrostatic potential probed by the 3D ED experiment.

Alkoxy-Bridged Dicopper(II) Cores Meet Tetracyanonickelate Linkers: Structural, Magnetic, and Theoretical Investigation of Cu/Ni Coordination Polymers

Two heterometallic Cu(II)/Ni(II) coordination polymers, [Cu2(Hbdea)2Ni(CN)4]n (1) and [Cu2(dmea)2Ni(CN)4]n·nH2O (2), were successfully self-assembled in water by reacting Cu(II) nitrate with H2bdea (N-butyldiethanolamine) and Hdmea (N,N-dimethylethanolamine) in the presence of sodium hydroxide and [Ni(CN)4]2-. These new coordination polymers were investigated by single-crystal and powder X-ray diffraction and fully characterized by FT-IR spectroscopy, thermogravimetry, elemental analysis, variable-temperature magnetic susceptibility measurements, and theoretical DFT and CASSCF calculations. Despite differences in crystal systems, in both compounds, each dinuclear building block [Cu2(μ-aminopolyalcoholate)2]2+ is bridged by diamagnetic [Ni(CN)4]2- linkers, resulting in 1D (1) or 2D (2) metal-organic architectures. Experimental magnetic studies show that both compounds display strong antiferromagnetic coupling (J = -602.1 cm-1 for 1 and -151 cm-1 for 2) between Cu(II) ions within the dimers mediated by the μ-O-alkoxo bridges. These results are corroborated by the broken symmetry DFT studies, which also provide further insight into the electronic structures of copper dimeric units. By reporting a facile self-assembly synthetic protocol, this study can be a model to widen a still limited family of heterometallic Cu/Ni coordination polymer materials with different functional properties.

Supramolecular assemblies of citalopram and escitalopram in β-cyclodextrin dimeric cavity: Crystallographic and theoretical insights

Cyclodextrin (CD) encapsulation improves physicochemical and pharmacological properties of selective serotonin reuptake inhibitors (SSRIs), which are efficacious in treating depression, a global mental health problem. Here, we scrutinize β-CD inclusion complexes with racemate citalopram (rac-CTP; 1) and escitalopram ((S)-CTP; 2) by combined single-crystal X-ray diffraction and DFT full-geometry optimization. X-ray analysis unveiled that the 2:2 inclusion complexes of 1 and 2 with similar inclusion modes and topologies are stabilized by various intermolecular interactions of host-guest CH···π, host-host OH···O H-bonds, and guest-guest F···F in the tail-to-tail dimeric asymmetric unit. In the crystals, these dimers are stacked on top of each other, yielding similar channel structures of distinct crystal symmetries, triclinic, P1 (1) and monoclinic, P21 (2), which are further maintained by guest-guest π···π and CN···π interactions. The thermodynamic stabilities evaluated by DFT calculation indicate the vital role of weak intermolecular interactions in the formation and stabilization of the β-CD monomeric and dimeric inclusion complexes. This study provides crystallographic and theoretical evidence for the improved stability and the masked bitterness of CTP through β-CD encapsulation as patented previously and suggests the pharmaceutical implications in the drug delivery and enantioseparation.

Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors

Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen-Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen-Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen-Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.

Concomitant polymorphs of 2-imino-2H-chromene-3-carboxylic acid amide: experimental and quantum chemical study

2-Iminocoumarin-3-carboxamide (2-imino-2 H-chromene-3-carboxylic acid) is a perspective compound for use in the pharmaceutical industry. This compound crystallized from several solvents as two concomitant polymorphic forms. The monoclinic polymorph, crystallized initially, is formed due to strong N-H...O hydrogen bonds, weak C-H...O and C-H...N(π) hydrogen bonds, and stacking interactions of `head-to-head' type. The triclinic polymorphic form obtained due to slow evaporation of the same solution is formed due to only strong intermolecular interactions, N-H...O hydrogen bonds of two types, and stacking interactions of two types. Analysis of pairwise interaction energies showed that the monoclinic structure is columnar while the triclinic one is layered. Calculations in a periodic approximation of their lattice energies confirmed that the monoclinic polymorphic crystals are metastable as compared to the stable triclinic polymorph. Further quantum chemical modeling of possible structure deformations proved that both concomitant polymorphs can not be transformed into a new polymorphic form under external influence.

Refinement of X-ray and electron diffraction crystal structures using analytical Fourier transforms of Slater-type atomic wavefunctions in Olex2

An implementation of Slater-type spherical scattering factors for X-ray and electron diffraction for elements in the range Z = 1-103 is presented within the software Olex2. Both high- and low-angle Fourier behaviour of atomic electron density and electrostatic potential can thus be addressed, in contrast to the limited flexibility of the four Gaussian plus constant descriptions which are currently the most widely used method for calculating atomic scattering factors during refinement. The implementation presented here accommodates the increasing complexity of the electronic structure of heavier elements by using complete atomic wavefunctions without any interpolation between precalculated tables or intermediate fitting functions. Atomic wavefunctions for singly charged ions are implemented and made accessible, and these show drastic changes in electron diffraction scattering factors compared with the neutral atom. A comparison between the two different spherical models of neutral atoms is presented as an example for four different kinds of X-ray and two electron diffraction structures, and comparisons of refinement results using the existing diffraction data are discussed. A systematic but slight improvement in R values and residual densities can be observed when using the new scattering factors, and this is discussed relative to effects on the atomic displacement parameters and atomic positions, which are prominent near the heavier elements in a structure.

Elucidating the Electronic Nature of Rh-based Paddlewheel Catalysts from 103 Rh NMR Chemical Shifts: Insights from Quantum Mechanical Calculations

The tremendous importance of dirhodium paddlewheel complexes for asymmetric catalysis is largely the result of an empirical optimization of the chiral ligand sphere about the bimetallic core. It was only recently that a H(C)Rh triple resonance 103 Rh NMR experiment provided the long-awaited opportunity to examine - with previously inconceivable accuracy - how variation of the ligands impacts on the electronic structure of such catalysts. The recorded effects are dramatic: formal replacement of only one out of eight O-atoms surrounding the metal centers in a dirhodium tetracarboxylate by an N-atom results in a shielding of the corresponding Rh-site of no less than 1000 ppm. The current paper provides the theoretical framework that allows this and related experimental observations made with a set of 19 representative rhodium complexes to be interpreted. In line with symmetry considerations, it is shown that the shielding tensor responds only to the donor ability of the equatorial ligands along the perpendicular principal axis. Axial ligands, in contrast, have no direct effect on shielding but may come into play via the electronicc i s ${cis}$ -effect that they exert onto the neighboring equatorial sites. On top of these fundamental interactions, charge redistribution within the core as well as the electronict r a n s ${trans}$ -effect of ligands of different donor strengths is reflected in the recorded 103 Rh NMR shifts.

Interrelations between Linkage Isomers of an Efficient Square-planar Nickel(II) Nitrite Photoswitch in the Solid State

An efficient nitrite nickel(II) photoswitch, with the 1-phenyl-2-hydroxyimino-3-[(2'-dimethylamino)ethyl]imino-1-propanone moiety used as the ancillary ligand, is reported. In the ground-state ('dark') crystal structure, the studied compound exists predominantly as the nitro-(η1 -N(O)2 ) isomer, however, traces of the exo- and endo-nitrito-(η1 -ONO) forms are detected both at 100 K (4-5 % each) and under ambient conditions (~9 % each). When excited with the 405-530 nm LED light, the nitro-to-nitrito isomerization takes place. The total conversion exceeds 90 %. The exo-nitrito linkage isomer constitutes the dominant photo-generated form, whereas the relative population of both nitrito species depends on temperature. The reaction is fully reversible and reproducible. The photo-products are stable up to 200 K. The system constitutes a good model case for the reaction mechanism studies. Thus, experimental and theoretical investigations on the photo-isomerism were conducted and are presented in detail. Eventually, the nitro→exo-nitrito→endo-nitrito reaction pathway is proposed.

1-(Pyridin-4-yl)-4-thiopyridine (PTP) in the crystalline state - pure PTP and a cocrystal and salt

The first in situ preparation and single-crystal structure identification of pure 1-(pyridin-4-yl)-4-thiopyridine (PTP), C10H8N2S, a simple and basic derivative of mercaptopyridine, from a crystallization mixture is described. The same PTP was found in two multicomponent crystal forms with 3,5-dinitrobenzoic acid as a classic two-component cocrystal, namely, 1-(pyridin-4-yl)-4-thiopyridine-3,5-dinitrobenzoic acid (1/1), C7H4N2O6·C10H8N2S, and with 2-hydroxy-3,5-dinitrobenzoic acid as a salt formed via proton transfer from the hydroxy group of the acid to the pyridyl N atom of PTP, namely, 4-(4-sulfanylidene-1,4-dihydropyridin-1-yl)pyridin-1-ium 1-carboxy-3,5-dinitrophenolate, C10H9N2S+·C7H3N2O7-. The protonation energy of PTP is 944.64 kJ mol-1, indicating slightly greater N-basicity compared to pyridine, a well characterized and very basic chemical reference. A variety of molecular interactions can be observed in the three new crystal structures of PTP, which are all discussed in detail. Our findings confirm those of previous studies, indicating that PTP and 4-mercaptopyridine may, under suitable conditions, be chemically converted to one another, and that this process can be stimulated by light (UV-Vis).

Improved joint X-ray and neutron refinement procedure in Phenix

Neutron diffraction is one of the three crystallographic techniques (X-ray, neutron and electron diffraction) used to determine the atomic structures of molecules. Its particular strengths derive from the fact that H (and D) atoms are strong neutron scatterers, meaning that their positions, and thus protonation states, can be derived from crystallographic maps. However, because of technical limitations and experimental obstacles, the quality of neutron diffraction data is typically much poorer (completeness, resolution and signal to noise) than that of X-ray diffraction data for the same sample. Further, refinement is more complex as it usually requires additional parameters to describe the H (and D) atoms. The increase in the number of parameters may be mitigated by using the `riding hydrogen' refinement strategy, in which the positions of H atoms without a rotational degree of freedom are inferred from their neighboring heavy atoms. However, this does not address the issues related to poor data quality. Therefore, neutron structure determination often relies on the presence of an X-ray data set for joint X-ray and neutron (XN) refinement. In this approach, the X-ray data serve to compensate for the deficiencies of the neutron diffraction data by refining one model simultaneously against the X-ray and neutron data sets. To be applicable, it is assumed that both data sets are highly isomorphous, and preferably collected from the same crystals and at the same temperature. However, the approach has a number of limitations that are discussed in this work by comparing four separately re-refined neutron models. To address the limitations, a new method for joint XN refinement is introduced that optimizes two different models against the different data sets. This approach is tested using neutron models and data deposited in the Protein Data Bank. The efficacy of refining models with H atoms as riding or as individual atoms is also investigated.

Neutron crystallographic refinement with REFMAC5 from the CCP4 suite

Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein-protein interactions. However, their direct visualization by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localization of only the most ordered H atoms at (sub-)atomic resolution (around 1.2 Å or higher). However, many H atoms of biochemical significance remain undetectable by this method. In contrast, neutron diffraction methods enable the visualization of most H atoms, typically in the form of deuterium (2H) atoms, at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought. REFMAC5 from the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of the CCP4 Monomer Library, the source of prior chemical information used in the refinement. One new feature for neutron data analysis in REFMAC5 is refinement of the protium/deuterium (1H/2H) fraction. This parameter describes the relative 1H/2H contribution to neutron scattering for hydrogen isotopes. The newly developed REFMAC5 algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) using either (i) neutron data only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement with REFMAC5 afforded models characterized by R-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy, especially for structures at medium-low resolution.

Halogen-Dependent Diversity and Weak Interactions in the Heterometallic Ni/Cd Complex Solids: Structural and Theoretical Investigation

Three novel heterometallic Ni/Cd coordination compounds [Ni(en)3][CdCl4]∙3dmso (1), [Ni(en)2(dmf)2][CdBr4] (2), and [Ni(en)3]2[CdI4](I)2 (3) have been synthesized through the self-assembly process in a one-pot reaction of cadmium oxide, nickel salt (or nickel powder), NH4X (X = Cl, Br, I), and ethylenediamine in non-aqueous solvents dmso (for 1) or dmf (for 2 and 3). Formation of the one- (1) or three-dimensional (2 and 3) hydrogen-bonded frameworks has been observed depending on the nature of the [CdX4]2- counter-anion, as well as on the nature of the solvent. The electronic structures of [Ni(en)3]2+ and [Ni(en)2(dmf)2]2+ cations were studied at the DFT and CASSCF levels, including the ab initio ligand field theory (AILFT) calculations. The non-covalent intermolecular contacts between the cationic nickel and anionic cadmium blocks in the solid state were investigated by the QTAIM analysis. The mechanism of ligand substitution at the nickel center in [Ni(en)2(dmf)2]2+ was theoretically investigated at the ωB97X-D4/ma-def2-TZVP//DLPNO-CCSD(T)/ma-def2-TZVPP level. The results demonstrate that thermodynamic factors are structure-determining ones due to low energy barriers of the rotation of dmf ligands in [Ni(en)2(dmf)2]2+ (below 3 kcal mol-1) and the reversible transformation of [Ni(en)2(dmf)2]2+ into [Ni(en)3]2+ (below 20 kcal mol-1).

Hydrogen Bonds Stabilize Chloroselenite Anions: Crystal Structure of a New Salt and Donor-Acceptor Bonding to SeO2

The single-crystal X-ray diffraction structure characterizing a new 4-methylbenzamidinium salt of chloroselenite [C8H11N2][ClSeO2] is reported. This is only the second crystal structure report on a ClSeO2- salt. The structure contains an extended planar hydrogen bond net, including a double interaction with both O atoms of the anion (an R228 ring in Etter notation). The anion has the shortest Se-Cl distances on record for any chloroselenite ion, 2.3202(9) Å. However, the two Se-O distances are distinct at 1.629(2) and 1.645(2) Å, attributed to weak anion-anion bridging involving the oxygen with the longer bond. DFT computations at the RB3PW91-D3/aug-CC-pVTZ level of theory reproduce the short Se-Cl distance in a gas-phase optimized ion pair, but free optimization of ClSeO2- leads to an elongation of this bond. A good match to a known value for [Me4N][ClSeO2] is found, which fits to the Raman spectroscopic evidence for this long-known salt and to data measured on solutions of the anion in CH3CN. The assignment of the experimental Raman spectrum was corrected by means of the DFT-computed vibrational spectrum, confirming the strong mixing of the symmetry coordinate of the Se-Cl stretch with both ν2 and ν4 modes.

2,6-Di-bromo-3,4,5-tri-meth-oxy-benzoic acid

The title compound, 2,6-di-bromo-3,4,5-tri-meth-oxy-benzoic acid (DBrTMBA), C10H10Br2O5, was obtained by bromination and transhalogenation of 2-iodo-3,4,5-tri-meth-oxy-benzoic acid with KBrO3. Like the previously reported 2,6-di-iodo-3,4,5-tri-meth-oxy-benzoic acid (DITMBA), the structure of the title compound features a catemeric arrangement of DBrTMBA mol-ecules along an endless chain of carb-oxy-lic H-carbonyl inter-actions. A short carbon-yl-phenyl contact hints at a possible lone pair(O)-π-hole inter-action further stabilizing the chain-like structure over a dimeric arrangement of the carb-oxy-lic acid.

Halogen Bond-Involving Self-Assembly of Iodonium Carboxylates: Adding a Dimension to Supramolecular Architecture

We designed 0D, 1D, and 2D supramolecular assemblies made of diaryliodonium salts (functioning as double σ-hole donors) and carboxylates (as σ-hole acceptors). The association was based on two charge-supported halogen bonds (XB), which occurred between IIII sites of the iodonium cations and the carboxylate anions. The sequential introduction of the carboxylic groups in the aryl ring of the benzoic acid added a dimension to the 0D supramolecular organization of the benzoate, which furnished 1D-chained and 2D-layered structures when terephthalate and trimesate anions, correspondingly, were applied as XB acceptors. The structure-directing XB were studied using DFT calculations under periodic boundary conditions and were followed by the one-electron-potential analysis and the Bader atoms-in-molecules topological analysis of electron density. These theoretical methods confirmed the existence of the XB and verified the philicities of the interaction partners in the designed solid-state structures.

Deciphering the driving forces in crystal packing by analysis of electrostatic energies and contact enrichment ratios

Hirshfeld surface analysis is a widely used tool for identifying the types of intermolecular contacts that contribute most significantly to crystal packing stabilization. One useful metric for analyzing these contacts is the contact enrichment descriptor, which indicates the types of contacts that are over- or under-represented. In this statistical study, enrichment ratios were combined with electrostatic energy (Eelec) data for a variety of compound families. To compute the electrostatic interaction energy between atoms, charge density models from the ELMAM2 database of multipolar atoms were used. As expected, strong hydrogen bonds such as O/N-H...N and O/N-H...O typically display large enrichment values and have the most negative (i.e. favorable) electrostatic energies. Conversely, contacts that are repulsive from an electrostatic perspective are usually the most under-represented. Analyzing the enrichment ratio and electrostatic energy indicators was shown to help identify which favorable contacts are the most competitive with each other. For weaker interactions, such as hydrophobic contacts, the behavior is less clear cut and can depend on other factors such as the chemical content of the molecule. The anticorrelation between contact enrichment and Eelec is generally lost for weaker contacts. However, we observed that C...C contacts are often enriched in crystal structures containing heterocycles, despite the low electrostatic attraction. For molecules with only weak hydrogen bond donors/acceptors and hydrophobic groups, the correlation between contact enrichment and Eelec is still evident for the strongest of these interactions. However, there are some exceptions where the most favorable contacts from an electrostatic perspective are not the most over-represented. This can occur in cases where the shape of the molecule is complex or elongated, favoring dispersion forces and shape complementarity in the packing.

Synthetic Study of Natural Metabolites Containing a Benzo[c]oxepine Skeleton: Heterocornol C and D

A versatile strategy for the enantioselective synthesis of a benzo[c]oxepine structural core containing natural secondary metabolites was developed. The key steps of the synthetic approach include ring-closing alkene metathesis for seven-member ring construction, the Suzuki-Miyaura cross-coupling reaction for the installation of the double bond and Katsuki-Sharpless asymmetric epoxidation for the introduction of chiral centers. The first total synthesis and absolute configuration assignment of heterocornol D (3a) were achieved. Four stereoisomers, 3a, ent-3a, 3b and ent-3b, of this natural polyketide were prepared, starting with 2,6-dihydroxy benzoic acid and divinyl carbinol. The absolute and relative configuration of heterocornol D was assigned via single-crystal X-ray analysis. The extension of the described synthetic approach is further presented with the synthesis of heterocornol C by applying the ether group reduction method to the lactone.

New Polymorphic Modifications of 6-Methyluracil: An Experimental and Quantum Chemical Study

Polymorphism of 6-methyluracil, which affects the regulation of lipid peroxidation and wound healing, has been studied by experimental and quantum chemical methods. Two known polymorphic modifications and two new crystalline forms were crystallized and characterized by single crystal and powder X-ray diffraction (XRD) methods as well as by the differential scanning calorimetry (DSC) method and infrared (IR) spectroscopy. The calculations of pairwise interaction energies between molecules and lattice energies in periodic boundary conditions have shown that the polymorphic form 6MU_I used in the pharmaceutical industry and two new forms 6MU_III and 6MU_IV, which can be formed due to temperature violations, may be considered as metastable. The centrosymmetric dimer bound by two N-H···O hydrogen bonds was recognized as a dimeric building unit in all of the polymorphic forms of 6-methyluracil. Four polymorphic forms have a layered structure from the viewpoint of interaction energies between dimeric building units. The layers parallel to the (100) crystallographic plane were recognized as a basic structural motif in the 6MU_I, 6MU_III, and 6MU_IV crystals. In the 6MU_II structure, a basic structural motif is a layer parallel to the (001) crystallographic plane. The ratio between the interaction energies within the basic structural motif and between neighboring layers correlates with the relative stability of the studied polymorphic forms. The most stable polymorphic form 6MU_II has the most anisotropic "energetic" structure, while the interaction energies in the least stable form 6MU_IV are very close in various directions. The modeling of shear deformations of layers in the metastable polymorphic structures has not revealed any possibility of these crystals to be deformed under external mechanical stress or pressure influence. These results allow the use of metastable polymorphic forms of 6-methyluracil in the pharmaceutical industry without any limitations.

The CCP4 suite: integrative software for macromolecular crystallography

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.

How cyclodextrin encapsulation improves molecular stability of apple polyphenols phloretin, phlorizin, and ferulic acid: Atomistic insights through structural chemistry

Phloretin (PRT), phlorizin (PRZ), and ferulic acid (FEA) prevalent in apples are unstable and less soluble in water, which can be improved by cyclodextrin (CD) encapsulation. This study aimed to provide atomistic insights of β-CD-PRT (1), β-CD-PRZ (2), and α-CD-FEA (3) complexes. Single-crystal X-ray diffraction (XRD) revealed that one PRZ (2) and one FEA (3) insert the aromatic B-ring and C=C-C=O(O) group respectively into the β-CD (2) and α-CD (3) cavities, whereas a half-occupied PRT (1) inserts the B-ring across the β-CD cavity. The induced-fit process yielded thermodynamically stable complexes 2 > 1 > 3, in agreement with the density functional theory (DFT)-optimized structures with the corresponding number of intermolecular OH···O H-bonds (7 > 3 > 1). Perpendicular conformations of the pharmaceutically active forms of PRT (1) and PRZ (2) are first observed crystallographically. This study confirmed the potential applications of CDs as molecular stabilizers and aqueous solubilizers for the improved bioavailability and efficient delivery of food bioactive compounds.

Accurate structure models and absolute configuration determination using dynamical effects in continuous-rotation 3D electron diffraction data

Continuous-rotation 3D electron diffraction methods are increasingly popular for the structure analysis of very small organic molecular crystals and crystalline inorganic materials. Dynamical diffraction effects cause non-linear deviations from kinematical intensities that present issues in structure analysis. Here, a method for structure analysis of continuous-rotation 3D electron diffraction data is presented that takes multiple scattering effects into account. Dynamical and kinematical refinements of 12 compounds-ranging from small organic compounds to metal-organic frameworks to inorganic materials-are compared, for which the new approach yields significantly improved models in terms of accuracy and reliability with up to fourfold reduction of the noise level in difference Fourier maps. The intrinsic sensitivity of dynamical diffraction to the absolute structure is also used to assign the handedness of 58 crystals of 9 different chiral compounds, showing that 3D electron diffraction is a reliable tool for the routine determination of absolute structures.

Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography

Structure analysis of small crystals is important in areas ranging from synthetic organic chemistry to pharmaceutical and material sciences, as many compounds do not yield large crystals. Here we present the detailed characterization of the structure of an organic molecule, rhodamine-6G, determined at a resolution of 0.82 Å by an X-ray free-electron laser (XFEL). Direct comparison of this structure with that obtained by electron crystallography from the same sample batch of microcrystals shows that both methods can accurately distinguish the position of some of the hydrogen atoms, depending on the type of chemical bond in which they are involved. Variations in the distances measured by XFEL and electron diffraction reflect the expected differences in X-ray and electron scatterings. The reliability for atomic coordinates was found to be better with XFEL, but the electron beam showed a higher sensitivity to charges.

Noncovalent Chelation by Halogen Bonding in the Design of Metal-Containing Arrays: Assembly of Double σ-Hole Donating Halolium with CuI-Containing O,O-Donors

Five new copper(I) complexes─composed of the paired dibenzohalolium and [CuL₂]^- (L = 1,2,4-oxadiazolate) counterions in which O,O-atoms of the anion are simultaneously linked to the halogen atom─were generated and isolated as the solid via the three-component reaction between [Cu(MeCN)₄](BF₄), sodium 1,2,4-oxadiazolates, and dibenzohalolium triflates (or trifluoroacetates). This reaction is different from the previously reported Cu^I-catalyzed arylation of 1,2,4-oxadiazolones by diaryliodonium salts. Inspection of the solid-state X-ray structures of the complexes revealed the strong three-center X···O,O (X = Br, I) halogen bonding occurred between the oxadiazolate moieties and dibenzohalolium cation. According to performed theoretical calculations, this noncovalent interaction (or noncovalent chelation) was recognized as the main force in the stabilization of the copper(I) complexes. An explanation for the different behavior of complexes, which provide either chelate or nonchelate binding, is based on the occurrence of additional -CH₃···π interactions, which were also quantified.

Ligand-Receptor Interactions of Lamivudine: A View from Charge Density Study and QM/MM Calculations

The nature and strength of interactions for an anti-HIV drug, Lamivudine, were studied in a pure crystal form of the drug and the ligand–receptor complexes. High-resolution single-crystal X-ray diffraction studies of the tetragonal polymorph allowed the drug’s experimental charge density distribution in the solid state to be obtained. The QM/MM calculations were performed for a simplified model of the Lamivudine complex with deoxycytidine kinase (two complexes with different binding modes) to reconstruct the theoretical charge density distribution. The peculiarities of intramolecular interactions were compared with previously reported data for an isolated molecule. Intermolecular interactions were revealed within the quantum theory of ‘Atoms in Molecules’, and their contributions to the total crystal energy or ligand–receptor binding energy were evaluated. It was demonstrated that the crystal field effect weakened the intramolecular interactions. Overall, the energies of intermolecular interactions in ligand–receptor complexes (320.1–394.8 kJ/mol) were higher than the energies of interactions in the crystal (276.9 kJ/mol) due to the larger number of hydrophilic interactions. In contrast, the sum of the energies of hydrophobic interactions was found to be unchanged. It was demonstrated by means of the Voronoi tessellation that molecular volume remained constant for different molecular conformations (250(13) Å3) and increased up to 399 Å3 and 521(30) Å3 for the Lamivudine phosphate and triphosphate.

Systematic Study of Podand Molecules for Synergistic Halogen and Hydrogen Bond-Driven Anion Recognition in the Solid State

The increasing demand of species for the efficient capture and sensing of anions benefits from a systematic study of anion binding capabilities in the solid state. This work reports a detailed crystallographic study of ten structurally related podands and shows that these charged receptors bind anions with a combination of charge-assisted halogen and hydrogen bonds. Computational tools helped in highlighting the role of the different involved interaction and afforded possible design principles for the design of improved podands.

Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time-accuracy trade-off

Aspherical atom refinement is the key to achieving accurate structure models, displacement parameters, hydrogen-bond lengths and analysis of weak interactions, amongst other examples. There are various quantum crystallographic methods to perform aspherical atom refinement, including Hirshfeld atom refinement (HAR) and transferable aspherical atom model (TAAM) refinement. Both HAR and TAAM have their limitations and advantages, the former being more accurate and the latter being faster. With the advent of non-spherical atoms in Olex2 (NoSpherA2), it is now possible to overcome some limitations, like treating disorder, twinning and network structures, in aspherical refinements using HAR, TAAM or both together. TAAM refinement in NoSpherA2 showed significant improvement in refinement statistics compared with independent atom model (IAM) refinements on a diverse set of X-ray diffraction data. The sensitivity of TAAM towards poor data quality and disorder was observed in terms of higher refinement statistics for such structures. A comparison of IAM with TAAM and HAR in NoSpherA2 indicated that the time taken by TAAM refinements was of the same order of magnitude as that taken by IAM, while in HAR the time taken using a minimal basis set was 50 times higher than for IAM and rapidly increased with increasing size of the basis sets used. The displacement parameters for hydrogen and non-hydrogen atoms were very similar in both HAR and TAAM refinements. The hydrogen-bond lengths were slightly closer to neutron reference values in the case of HAR with higher basis sets than in TAAM. To benefit from the advantages of each method, a new hybrid refinement approach has been introduced, allowing a combination of IAM, HAR and TAAM in one structure refinement. Refinement of coordination complexes involving metal-organic compounds and network structures such as covalent organic frameworks and metal-organic frameworks is now possible in a hybrid mode such as IAM-TAAM or HAR-TAAM, where the metal atoms are treated via either the IAM or HAR method and the organic part via TAAM, thus reducing the computational costs without compromising the accuracy. Formal charges on the metal and ligand can also be introduced in hybrid-mode refinement.

Aryl Boronic Acids in Columnar Stacked Co-crystalline Materials: Key-Factors Governing the Assembly with Quinones

The assembly of aryl boronic acids B with quinones Q into columnar mixed stacked materials, as previously observed in the solid-state, has been here subjected to a detailed theoretical analysis focusing on the properties of the isolated synthons (HOMO-LUMO energies, electron affinity, ionization potential, reorganization hole/electron energies, partial Hirshfeld atomic charges and conformation stabilities) as well as those of the 1 : 1 adducts (Hirshfeld analysis, IRI surfaces, Hirshfeld atomic charges, hydrogen bond and slipped stacked π-π contributions). The overall picture obtained throught this study shows an intricate pattern of interconnected factors contributing to the formation and stability of the B_x Q_y adducts, and it unveils the importance of parameters such as HOMO-LUMO gap, polarization and charge transfer, in addition to the more evident hydrogen bond and slipped-stacked π-π interactions in the formation of 1 : 1 adducts. An explanation has been also given for the presence in some B_x Q_y adducts of the rare anti-anti conformation for the BO-H group with respect to the most studied and common anti-syn conformation.

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).

Structure and charge analysis of a cyclic aluminium hydride: cyclo-1,5-bis-μ-dimethylamino-3,7-di-μ-hydrido-2,4,6,8-tetrakis(dimethylaluminium)

The title compound, [Al4(CH3)8(C2H7N)2H2], crystallizes as eight-membered rings with -(CH3)2Al-(CH3)2N-(CH3)2Al- moieties connected by single hydride bridges. In the X-ray structure, the ring has a chair conformation, with the hydride H atoms being close to the plane through the four Al atoms. An optimized structure was also calculated by all-electron density functional theory (DFT) methods, which agrees with the X-ray structure but gives a somewhat different geometry for the hydride bridge. Charges on the individual atoms were determined by valence shell occupancy refinements using MoPro and also by DFT calculations analyzed by several different methods. All methods agree in assigning a positive charge to the Al atoms, negative charges to the C, N, and hydride H atoms, and small positive charges to the methyl H atoms.

Acetophenone-Based 3,4-Dihydropyrimidine-2(1H)-Thione as Potential Inhibitor of Tyrosinase and Ribonucleotide Reductase: Facile Synthesis, Crystal Structure, In-Vitro and In-Silico Investigations

The acetophenone-based 3,4-dihydropyrimidine-2(1H)-thione was synthesized by the reaction of 4-methylpent-3-en-2-one (1), 4-acetyl aniline (2) and potassium thiocyanate. The spectroscopic analysis including: FTIR, 1H-NMR, and single crystal analysis proved the structure of synthesized compound (4), with the six-membered nonplanar ring in envelope conformation. In crystal structure, the intermolecular N-H ⋯ S and C-H ⋯ O hydrogen bonds link the molecule in a two-dimensional manner which is parallel to (010) the plane enclosing R22 (8) and R22 (10) ring motifs. After that, the Hirshfeld surfaces and their related two-dimensional fingerprint plots were used for thorough investigation of intermolecular interactions. According to Hirshfeld surface analysis, the most substantial contributions to the crystal packing are from H ⋯ H (59.5%), H ⋯ S/S ⋯ H (16.1%), and H ⋯ C/C ⋯ H (13.1%) interactions. The electronic properties and stability of the compound were investigated through density functional theory (DFT) studies using B3LYP functional and 6-31G* as a basis set. The compound 4 displayed the high chemical reactivity with chemical softness of 2.48. In comparison to the already reported known tyrosinase inhibitor, the newly synthesized derivatives exhibited almost seven-fold better inhibition of tyrosinase (IC50 = 1.97 μM), which was further supported by molecular docking studies. The compound 4 inside the active pocket of ribonucleotide reductase (RNR) exhibited a binding energy of -19.68 kJ/mol, and with mammalian deoxy ribonucleic acid (DNA) it acts as an effective DNA groove binder with a binding energy of -21.32 kJ/mol. The results suggested further exploration of this compound at molecular level to synthesize more potential leads for the treatment of cancer.

N-(4-Methyl-3-((4-(pyridin-3-yl)pyrimidin-2-yl)amino)phenyl)-4-((4-methylpiperazin-1-yl)methyl)benzamide

Imatinib is one of the most used therapeutic agents to treat leukemia, which specifically inhibits the activity of tyrosine kinases. This polytopic molecule has been structurally characterized only in the form of its piperazin-1-ium salt (mesylate, picrate, citrate, fumarate or malonate). Herein we present the crystal structure of the freebase Imatinib which precipitated from a 1:10 mixture with arginine. The molecule realizes an extended conformation and forms infinite H-bonded chains through its amide, amine and pyrimidine groups.

Searching for correlations between geometric and spectroscopic parameters of intramolecular hydrogen bonds in porphyrin-like macrocycles

Chemical bond lengths and angles are characteristic structural parameters of a molecule. Similarly, the frequencies of the vibrational modes and the NMR chemical shifts are unique "chemical fingerprints" specific to a compound. These are the basic parameters describing newly obtained compounds and enabling their identification. Intramolecular hydrogen bonding significantly influences the physicochemical properties of macrocyclic compounds with a porphyrin-like structure. This work presents the verification for correlations between geometric and spectroscopic parameters related to hydrogen bonds in this type of macrocyclic compounds. In particular, such relationships were investigated for a large group of porphyrin, porphycene, and dibenzotetraaza[14]annulene derivatives and a group of other macrocycles with similar structure. A very strong linear correlation was found only between the vibrational frequencies of the NH groups involved in a hydrogen bond and the length of this bond, which applied to all macrocyclic compounds of this type. Several other relationships were found between spectroscopic (IR, Raman, NMR) and geometric (X-ray) parameters, highlighting differences and similarities between different families of macrocycles. Apart from providing a better understanding of the nature of hydrogen bonds and their characteristics in porphyrin-like macrocyclic compounds, these relationships will facilitate the identification of new macrocycles and the extrapolation of their spectroscopic properties.

Water: new aspect of hydrogen bonding in the solid state

All water-water contacts in the crystal structures from the Cambridge Structural Database with d OO ≤ 4.0 Å have been found. These contacts were analysed on the basis of their geometries and interaction energies from CCSD(T)/CBS calculations. The results show 6729 attractive water-water contacts, of which 4717 are classical hydrogen bonds (d OH ≤ 3.0 Å and α ≥ 120°) with most being stronger than -3.3 kcal mol-1. Beyond the region of these hydrogen bonds, there is a large number of attractive interactions (2062). The majority are antiparallel dipolar interactions, where the O-H bonds of two water molecules lying in parallel planes are oriented antiparallel to each other. Developing geometric criteria for these antiparallel dipoles (β1, β2 ≥ 160°, 80 ≤ α ≤ 140° and T HOHO > 40°) yielded 1282 attractive contacts. The interaction energies of these antiparallel oriented water molecules are up to -4.7 kcal mol-1, while most of the contacts have interaction energies in the range -0.9 to -2.1 kcal mol-1. This study suggests that the geometric criteria for defining attractive water-water interactions should be broader than the classical hydrogen-bonding criteria, a change that may reveal undiscovered and unappreciated interactions controlling molecular structure and chemistry.

Influence of modelling disorder on Hirshfeld atom refinement results of an organo-gold(I) compound

Details of the validation of disorder modelling with Hirshfeld atom refinement (HAR) for a previously investigated organo-gold(I) compound are presented here. The impact of refining disorder on HAR results is discussed using an analysis of the differences of dynamic structure factors. These dynamic structure factor differences are calculated from thermally smeared quantum mechanical electron densities based on wavefunctions that include or exclude electron correlation and relativistic effects. When disorder is modelled, the electron densities stem from a weighted superposition of two (or more) different conformers. Here this is shown to impact the relative importance of electron correlation and relativistic effect estimates expressed by the structure factor magnitudes. The role of disorder modelling is also compared with the effect of the treatment of hydrogen anisotropic displacement parameter (ADP) values and atomic anharmonicity of the gold atom. The analysis of ADP values of gold and disordered carbon atoms showed that the effect of disorder significantly altered carbon ADP values and did not influence those of the gold atom.