Refinement of macromolecular structures against neutron data with SHELXL2013

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.

Electron crystallography and dedicated electron-diffraction instrumentation

Electron diffraction (known also as ED, 3D ED or microED) is gaining momentum in science and industry. The application of electron diffraction in performing nano-crystallography on crystals smaller than 1 µm is a disruptive technology that is opening up fascinating new perspectives for a wide variety of compounds required in the fields of chemical, pharmaceutical and advanced materials research. Electron diffraction enables the characterization of solid compounds complementary to neutron, powder X-ray and single-crystal X-ray diffraction, as it has the unique capability to measure nanometre-sized crystals. The recent introduction of dedicated instrumentation to perform ED experiments is a key aspect of the continued growth and success of this technology. In addition to the ultra-high-speed hybrid-pixel detectors enabling ED data collection in continuous rotation mode, a high-precision goniometer and horizontal layout have been determined as essential features of an electron diffractometer, both of which are embodied in the Eldico ED-1. Four examples of data collected on an Eldico ED-1 are showcased to demonstrate the potential and advantages of a dedicated electron diffractometer, covering selected applications and challenges of electron diffraction: (i) multiple reciprocal lattices, (ii) absolute structure of a chiral compound, and (iii) R-values achieved by kinematic refinement comparable to X-ray data.

Correlated Rattling of Sodium-Chains Suppressing Thermal Conduction in Thermoelectric Stannides

Tin-based intermetallics with tunnel frameworks containing zigzag Na chains that excite correlated rattling impinging on the framework phonons are attractive as thermoelectric materials owing to their low lattice thermal conductivity. The correlated rattling of Na atoms in the zigzag chains and the origin of the low thermal conductivity is uncovered via experimental and computational analyses. The Na atoms behave as oscillators along the tunnel, resulting in substantial interactions between Na atoms in the chain and between the chain and framework. In these intermetallic compounds, a shorter inter-rattler distance results in lower thermal conductivity, suggesting that phonon scattering by the correlated rattling Na-chains is enhanced. These results provide new insights into the behavior of thermoelectric materials with low thermal conductivity and suggest strategies for the development of such materials that utilize the correlated rattling.

Unusual core engineering on a copper hydride nanoball

A neutral polyhydrido copper cluster, [Cu₂₇H₁₅{S₂CNⁿBu₂}₁₂] (abbreviated as [Cu₂₇H₁₅]), was prepared by the reaction of dithiocarbamates (dtc), Cu(I) salts and NaBH₄. The isolated cluster provides insights into core engineering, demonstrating its novel ability to reversibly add or remove one copper atom from the cluster core. Single-crystal X-ray analysis reveals that the new core-shell structure exhibits a Cu₂₄ rhombicuboctahedral outer cage and an inner Cu₃ triangular kernel. The two core-shell clusters, [Cu₂₇H₁₅{S₂CNⁿBu₂}₁₂] and previously published [Cu₂₈H₁₅(S₂CNⁿBu₂)₁₂]⁺ (abbreviated as [Cu₂₈H₁₅]⁺), are only differentiated by one copper atom in their inner core. Importantly, we demonstrate core engineering with the controllable reversible transition between an irregular Cu₄ tetrahedron and a Cu₃ triangle, whilst maintaining their outer Cu₂₄ shell intact. The 15 hydride atoms in [Cu₂₇H₁₅], coordinated in three different modes, are co-incident with the hydride positions in [Cu₂₈H₁₅]⁺. The degradation of [Cu₂₇H₁₅] in solution or the addition of one eq. of Cu(I) ions leads to the conversion of [Cu₂₇H₁₅] into [Cu₂₈H₁₅]⁺, while the reverse transformation can be achieved by the addition of either formic acid or a reducing agent to [Cu₂₈H₁₅]⁺. A dicationic species was observed in the ESI mass spectrum, and the composition is formulated as [Cu₅₆H₃₀(S₂CNⁿBu₂)₂₄]²⁺, a dimer of [Cu₂₇H₁₅(S₂CNⁿBu₂)₁₂ + Cu⁺]₂²⁺. The dimeric species was further explored by DFT calculations, suggesting that the lowest energy structure consists of a [Cu₂₈H₁₅]⁺ and a [Cu₂₇H₁₅] cluster connected through one Cu⁺ atom bridge. As a result, [Cu₂₇H₁₅] is considered an intermediate species in the formation of the more stable [Cu₂₈H₁₅]⁺ nanoball.

Latonduine-1-Amino-Hydantoin Hybrid, Triazole-Fused Latonduine Schiff Bases and Their Metal Complexes: Synthesis, X-ray and Electron Diffraction, Molecular Docking Studies and Antiproliferative Activity

A series of latonduine derivatives, namely 11-nitro-indolo[2,3-d]benzazepine-7-(1-amino-hydantoin) (B), triazole-fused indolo[2,3-d]benzazepine-based Schiff bases HL1 and HL2 and metal complexes [M(p-cymene)(HL1)Cl]Cl, where M = Ru (1), Os (2), and [Cu(HL2)Cl2] (3) were synthesized and characterized by spectroscopic techniques (UV–vis, 1H, 13C, 15N–1H HSQC NMR) and ESI mass spectrometry. The molecular structures of B and HL1 were confirmed by single-crystal X-ray diffraction, while that of 3 by electron diffraction of nanometer size crystalline sample. Molecular docking calculations of species B in the binding pocket of PIM-1 enzyme revealed that the 1-amino-hydantoin moiety is not involved in any hydrogen-bonding interactions, even though a good accommodation of the host molecule in the ATP binding pocket of the enzyme was found. The antiproliferative activity of organic compounds B, HL1 and HL2, as well as complexes 1–3 was investigated in lung adenocarcinoma A549, colon adenocarcinoma LS-174 and triple-negative breast adenocarcinoma MDA-MB-231 cells and normal human lung fibroblast cells MRC-5 by MTT assays; then, the results are discussed.

A quinazolin-based Schiff-base chemosensor for colorimetric detection of Ni2+ and Zn2+ ions and 'turn-on' fluorometric detection of Zn2+ ion

Herein, we have reported a novel quinazolin-based Schiff base chemosensor (E)-2-benzamido-N'-(1-(pyridin-2-yl)ethylidene)benzohydrazide (L). L has been designed, synthesised and characterised by ¹H-NMR, IR spectroscopy, ESI-MS spectrometry and theoretical studies. The receptor showed appreciable colorimetric λ _max shift for both Ni²⁺ and Zn²⁺ ions and fluorometric "turn on" response in presence of only Zn²⁺ ion. The Jobs plot analysis revealed that receptor forms 2 : 1 complex with both the ions Ni²⁺ and Zn²⁺, further confirmed by ESI-MS analysis. The single crystal structure of L-Ni²⁺ complex (1) has also been determined. The colorimetric detection limits were calculated to 7.9 nM and 7.5 nM respectively for Ni²⁺ and Zn²⁺ in methanol-Tris-HCl buffer medium (10 mM, pH 7.2, 1 : 1 v/v). The chemosensor L can be applied for the recovery of contaminated water samples.

Surface modifications of eight-electron palladium silver superatomic alloys

Atomically precise thiolate-protected coinage metal nanoclusters and their alloys are far more numerous than their selenium congeners, the synthesis of which remains extremely challenging. Herein, we report the synthesis of a series of atomically defined dithiophosph(in)ate protected eight-electron superatomic palladium silver nanoalloys [PdAg₂₀{S₂PR₂}₁₂], 2a-c (where R = OⁱPr, a; OⁱBu, b; Ph, c) via ligand exchange and/or co-reduction methods. The ligand exchange reaction on [PdAg₂₀{S₂P(OⁿPr)₂}₁₂], 1, with [NH₄{Se₂PR₂}₁₂] (where R = OⁱPr, or OⁿPr) leads to the formation of [PdAg₂₀{Se₂P(OⁱPr)₂}₁₂] (3) and [PdAg₂₀{Se₂P(OⁿPr)₂}₁₂] (4), respectively. Solid state structures of 2a, 2b, 3 and 4 unravel different PdAg₂₀ metal frameworks from their parent cluster, originating from the different distributions of the eight-capping silver(I) atoms around a Pd@Ag₁₂ centered icosahedron with C_2, D_3, T_h and T_h symmetries, respectively. Surprisingly ambient temperature crystallization of the reaction product 3 obtained by the ligand exchange reaction on 1 has resulted in the co-crystallization of two isomers in the unit cell with overall T (3a) and C₃ (3b) symmetries, respectively. To our knowledge, this is the first ever characterized isomeric pair among the selenolate-protected NCs. Density functional theory (DFT) studies further rationalize the preferred geometrical isomerism of the PdAg₂₀ core.

Hydrogens and hydrogen-bond networks in macromolecular MicroED data

Microcrystal electron diffraction (MicroED) is a powerful technique utilizing electron cryo-microscopy (cryo-EM) for protein structure determination of crystalline samples too small for X-ray crystallography. Electrons interact with the electrostatic potential of the sample, which means that the scattered electrons carry information about the charged state of atoms and provide relatively stronger contrast for visualizing hydrogen atoms. Accurately identifying the positions of hydrogen atoms, and by extension the hydrogen bonding networks, is of importance for understanding protein structure and function, in particular for drug discovery. However, identification of individual hydrogen atom positions typically requires atomic resolution data, and has thus far remained elusive for macromolecular MicroED. Recently, we presented the ab initio structure of triclinic hen egg-white lysozyme at 0.87 Å resolution. The corresponding data were recorded under low exposure conditions using an electron-counting detector from thin crystalline lamellae. Here, using these subatomic resolution MicroED data, we identified over a third of all hydrogen atom positions based on strong difference peaks, and directly visualize hydrogen bonding interactions and the charged states of residues. Furthermore, we find that the hydrogen bond lengths are more accurately described by the inter-nuclei distances than the centers of mass of the corresponding electron clouds. We anticipate that MicroED, coupled with ongoing advances in data collection and refinement, can open further avenues for structural biology by uncovering the hydrogen atoms and hydrogen bonding interactions underlying protein structure and function.

Sodium β-Diketonate Glyme Adducts as Precursors for Fluoride Phases: Synthesis, Characterization and Functional Validation

Very few sodium complexes are available as precursors for the syntheses of sodium-based nanostructured materials. Herein, the diglyme, triglyme, and tetraglyme (CH₃O(CH₂CH₂O)_nCH₃, n = 2–4) adducts of sodium hexafluoroacetylacetonate were synthesized in a single-step reaction and characterized by IR spectroscopy, ¹H, and ¹³C NMR. Single-crystal X-ray diffraction studies provide evidence of the formation of the ionic oligomeric structure [Na₄(hfa)₆]²⁻•2[Na(diglyme₂]⁺ when the diglyme is coordinated, while a mononuclear seven-coordinated complex Na(hfa)•tetraglyme is formed with the tetraglyme. Reaction with the monoglyme (CH₃OCH₂CH₂OCH₃) does not occur, and the unadducted polymeric structure [Na(hfa)]_n forms, while the triglyme gives rise to a liquid adduct, Na(hfa)•triglyme•H₂O. Thermal analysis data reveal great potentialities for their applications as precursors in metalorganic chemical vapor deposition (MOCVD) and sol-gel processes. As a proof-of-concept, the Na(hfa)•tetraglyme adduct was successfully applied to both the low-pressure MOCVD and the sol-gel/spin-coating synthesis of NaF films.

Visualizing the Entire Range of Noncovalent Interactions in Nanocrystalline Hybrid Materials Using 3D Electron Diffraction

Noncovalent interactions are essential in the formation and properties of a diverse range of hybrid materials. However, reliably identifying the noncovalent interactions in nanocrystalline materials remains challenging using conventional methods such as X-ray diffraction and spectroscopy. Here, we demonstrate that accurate atomic positions including hydrogen atoms can be determined using three-dimensional electron diffraction (3D ED), from which the entire range of noncovalent interactions in a nanocrystalline aluminophosphate hybrid material SCM-34 are directly visualized. The protonation states of both the inorganic and organic components in SCM-34 are determined from the hydrogen positions. All noncovalent interactions, including hydrogen-bonding, electrostatic, π–π stacking, and van der Waals interactions, are unambiguously identified, which provides detailed insights into the formation of the material. The 3D ED data also allow us to distinguish different types of covalent bonds based on their bond lengths and to identify an elongated terminal P=O π-bond caused by noncovalent interactions. Our results show that 3D ED can be a powerful tool for resolving detailed noncovalent interactions in nanocrystalline materials. This can improve our understanding of hybrid systems and guide the development of novel functional materials.

Pentanuclear MII–MnII (M = Ni and Cu) complexes of N2O2 donor ligands with a variation of carboxylate anions: syntheses, structures, magnetic properties and catecholase-like activities

One NiII2MnII3 and two CuII2MnII3 complexes have been synthesized using N2O2 donor ligands. The former complex exhibits spin crossover at 2 K temperature. All the complexes exhibit catecholase-like activities.

Cu(II)(PhOMe-Salophen) Complex: Greener Pasture Biological Study, XRD/HAS Interactions, and MEP

PhOMe-salophen (1b) (salophen is N,N-bis(salycilidene)-1,2-phenylenediamine with two tert-butyl on each ring) and Cu(II) complex with PhOMe-salophen (1c) have been synthesized and characterized using various tools, including X-ray diffraction for the Cu(II)-complex (1c, C₄₃H₅₂CuN₂O₃)). The copper complex has been obtained by Cu²⁺ templated approach using 1b. PhOMe-salophen (1b) has been obtained in reasonably high yield using a mixture of the Schiff-base, 1a, Pd(OAc)₂, PPh₃, Na₂CO₃, 4-methoxyphenylboronic acid in benzene. We focus in this research work on the electronic and structural properties of the Cu–Schiff base complex. The tetra-coordinate τ₄ index was calculated, indicating almost a perfect square planner in agreement with X-ray diffraction results. MEP reveals the maximum positive regions in 1/-associated with the azomethine and methoxyphenyl C–H bonds with an average value of 0.03 a.u. Hirshfeld surface analysis (HSA) was also studied to highlight the significant inter-atomic contacts and their percentage contribution through 2D Fingerprint plot. In a fair comparative molecular docking study, 1b and 1c were docked together with N-[{(5-methylisoxazol-3-yl)-carbonyl}alanyl}-l-valyl]-N1-((1R,2Z)-4-(benzyloxy)-4-oxo-1-[{(3R)-2-oxopyrrolidin-3-yl}methyl]but-2-enyl)-l-leucinamide, N3 against main protease M^pro, (PDB code 7BQY) using the same parameters and conditions. Interesting here to use the free energy, in silico, molecular docking approach, which aims to rank our molecules with respect to the well-known inhibitor, N3. The binding scores of 1b, 1c, N3 are –7.8, –9.0, and –8.4 kcal/mol, respectively. These preliminary results propose that ligands deserve additional study in the context of possible remedial agents for COVID-19.

Alloying dichalcogenolate-protected Ag21 eight-electron nanoclusters: a DFT investigation

The isoelectronic doping of dichalcogenolato nanoclusters of the type [Ag₂₁{E₂P(OR)₂}₁₂]⁺ (E = S, Se) by any heteroatom belonging to groups 9-12 was systematically investigated using DFT calculations. Although they can differ in their global structure, all of these species have the same M@M₁₂-centered icosahedral core. In any case, the different structure types are all very close in energy. In all of them, three different alloying sites can be identified (central, icosahedral, peripheral) and calculations allowed the trends in heteroatom site occupation preference across the group 9-12 family to be revealed. These trends are supported by complementary experimental results. They were rationalized on the basis of electronegativity, potential involvement in the bonding of valence d-orbitals and atom size. TD-DFT calculations showed that the effect of doping on optical properties is sizable and this should stimulate research on the modulation of luminescence properties in the dithiolato and diseleno families of complexes.

Microcrystal electron diffraction in macromolecular and pharmaceutical structure determination

Microcrystal electron diffraction (MicroED) has recently shown to be a promising technique for structure determination in structural biology and pharmaceutical chemistry. Here, we discuss the unique properties of electrons and motivate its use for diffraction experiments. We review the latest developments in MicroED, and illustrate its applications in macromolecular crystallography, fragment screening and structure guided drug discovery. We discuss the perspectives of MicroED in synthetic chemistry and pharmaceutical development. We anticipate that the rapid advances MicroED showcased here will promote further development of electron crystallography and open up new opportunities for drug discovery.

Electrochemical sensing of hydrogen peroxide on a carbon paste electrode modified by a silver complex based on the 1,3-bis(1H-benzimidazole-2-yl)propane ligand

A new carbon paste electrode (Ag-CPE) modified with a nitrogen heterocyclic silver(I) complex, [Ag2(BBP)2](pic)2·CH3OH (BBP = 1,3-bis(1H-benzimidazol-2-yl)propane, pic = picrate), was developed as a highly sensitive and simple electrochemical sensor for the determination of hydrogen peroxide. The Ag(I) complex was prepared by an interface reaction and characterized by elemental analysis, IR and UV/Vis spectra and single crystal X-ray diffraction. The Ag(I) complex shows a dinuclear cluster structure, which is formed by two BBP ligands bridging two Ag (I) centers and an Ag–Ag interaction (d Ag–Ag = 3.0875 Å). Cyclic voltammetry and chronoamperometry studies showed that the electrochemical sensing performance of Ag-CPE for H2O2 was improved in 0.2 m phosphate buffer solution (PBS, pH = 6). The electrochemical H2O2 sensor Ag-CPE exhibits a wide linear detection range from 0.5 to 4.0 mm and a lower detection limit of 0.39 μm with a relatively high sensitivity of 6.77 μA mm −1. Moreover, the sensor also shows good anti-interference properties and stability. The results prove that the Ag(I) complex based on the bis(benzimidazole) ligand may be an efficient component of electrode materials.

Interplay of Halogen and Hydrogen Bonding through Co-Crystallization in Pharmacologically Active Dihydropyrimidines: Insights from Crystal Structure and Energy Framework

A solvent-assisted grinding method has been used to prepare co-crystals in substituted dihydropyrimidines (DHPM) that constitutes pharmacologically active compounds. These were characterized using FT-IR, PXRD, and single-crystal X-ray diffraction. In order to explore the possibility of formation of halogen (XB) and hydrogen bonding (HB) synthons in the solid state, co-crystallization attempts of differently substituted DHPM molecules, containing nitro, hydoxy, and chloro substituents, with different co-formers, such as 1,4-diiodo tetrafluorobenzene (1,4 DITFB) and 3-nitrobenzoic acid (3 NBA) were performed. The XB co-crystals (C2aXB, C2bXB, and C2cXB) prefer the formation of C-I⋅⋅⋅O/C-I⋅⋅⋅S XB synthon, whereas the HB co-crystal (C2dHB) is stabilized by N-H⋅⋅⋅O H-bond formation. Hirshfeld surface analysis revealed that the percentage contribution of intermolecular interactions for XB co-crystals prefer equal contribution of XB synthon along with HB synthon. Furthermore, the interaction energy was analyzed using energy frameworks, which suggests that their stability, a combination of electrostatics and dispersion, is enhanced through XB/HB in comparison to the parent DHPMs.

Isolation of a Nitromethane Anion in the Calix-Shaped Inorganic Cage

A calix-shaped polyoxometalate, [V₁₂O₃₂]⁴⁻ (V12), stabilizes an anion moiety in its central cavity. This molecule-sized container has the potential to control the reactivity of an anion. The highly-reactive cyanate is smoothly trapped by V12 to form [V₁₂O₃₂(CN)]⁵⁻. In the CH₃NO₂ solution, cyanate abstracts protons from CH₃NO₂, and the resultant CH₂NO₂⁻ is stabilized in V12 to form [V₁₂O₃₂(CH₂NO₂)]⁵⁻ (V12(CH₂NO₂)). A crystallographic analysis revealed the double-bond characteristic short bond distance of 1.248 Å between the carbon and nitrogen atoms in the nitromethane anion in V12. ¹H and ¹³C NMR studies showed that the nitromethane anion in V12 must not be exchanged with the nitromethane solvent. Thus, the V12 container restrains the reactivity of anionic species.

Modulation of Nuclearity in CuII -MnII Complexes of a N2 O2 Donor Ligand Depending upon Carboxylate Anions: Structures, Magnetic Properties and Catalytic Oxidase Activities

Three new hetero-metallic copper(II)-manganese(II) complexes, [(CuL)₂ Mn₃ (C₆ H₅ CO₂ )₆ ] (1), [(CuL)₂ Mn(CH₃ CO₂ )₂ ] (2), and {[(CuL)₂ Mn(C₆ H₅ CH₂ CO₂ )₂ ] ⋅ 2CH₃ CN} (3), have been synthesized using [CuL] as ''metalloligand'' (where H₂ L=N,N'-bis(2-hydroxynaphthyl-methylidene)-1,3-propanediamine). Single-crystal structural analyses show an almost linear penta-nuclear structure for complex 1 where a square planar [CuL] unit is connected to each of the two terminal Mn^II ions of a linear, centrosymmetric [Mn₃ (benzoate)₆ ] unit through the double phenoxido bridges. Both complexes 2 and 3 possess a linear tri-nuclear structure where two terminal square-pyramidal [CuL] units are bonded to the central Mn^II ion through double phenoxido oxygen atoms along with a syn-syn bridging acetate (for 2)/phenyl acetate (for 3). All three complexes exhibit catecholase, and phenoxazinone synthase-like activities under aerial conditions. For catecholase like activity, the turnover numbers (k_cat ) are 595, 40, and 205 h^-1 whereas, for phenoxazinone synthase like activity, the turnover numbers are 25, 4, and 11 h^-1 for complexes 1-3, respectively. The mechanism of both catalytic oxidase activities is proposed on the basis of mass spectral evidences. Variable-temperature (2-300 K) dc molar magnetic susceptibility measurements of 1 reveal antiferromagnetic interactions between the Cu-Mn centres (J₁ =-29.3 cm^-1 ), and also between the Mn-Mn centres of the [Mn₃ (benzoate)₆ ] unit (J₂ =-0.68 cm^-1 ). On increasing the magnetic field at 2 K, its ground spin state changes from S=3/2 to S=5/2 at 4 T, attributable to the low value of J₂ which makes the excited spin states close in energy with the ground spin state. Complexes 2 and 3 show antiferromagnetic coupling interactions between the Cu-Mn pairs with J values of -9.51, and -5.32 cm^-1 , respectively.

Joining of Trinuclear Heterometallic CuII2-MII (M = Mn, Cd) Nodes by Nicotinate to Form 1D Chains: Magnetic Properties and Catalytic Activities

In the present work, four new heterometallic coordination complexes, {[(CuL)₂Mn(nic)(H₂O)₂](ClO₄)(0.5H₂O)}_n (1), {[(CuL)₂Cd(nic)(H₂O)₂](ClO₄)(H₂O)}_n (2), [(CuL)₂Mn(nic)₂]·2CH₃OH (3), and [(CuL)₂Cd(nic)₂]·2CH₃OH (4) (where H₂L = N,N'-bis(α-methylsalicylidene)-1,3-propanediamine and nic = nicotinate ion), have been synthesized and characterized by single-crystal X-ray crystallography. In complexes 1 and 2, the nicotinate ion acts as a bifunctional linker (N,O donor) and joins the linear trinuclear nodes to form 1D polymeric chains. However, in complexes 3 and 4, the nicotinate ion uses only the oxygen atoms of the carboxylic acid (O donor) to bind to the metal centers, forming discrete linear trinuclear units, while the pyridyl nitrogen (N donor atom) remains free. The dc magnetic susceptibility measurements show that the Cu^II and Mn^II ions are antiferromagnetically coupled in both 1 and 3, with exchange coupling constants (J_Mn-Cu) of -20.57 ± 0.08 and -9.38 ± 0.08 cm^-1, respectively. Among the four complexes, 1 and 3 show catechol oxidase and phenoxazinone synthase like catalytic activities. The turnover numbers (k_cat) of complexes 1 and 3 for catecholase activity are 1121 and 720 h^-1, respectively, at an optimum pH of 8.0 and for phenoxazinone synthase activity are 429 and 398 h^-1, respectively, at an optimum pH of 9.7. The higher k_cat values of 1 for both reactions are attributable to a water molecule coordinated to the central Mn^II atom that facilitates the substrate-catalyst binding. An ESI-mass spectral analysis indicates that trinuclear heterometallic species, e.g., [(CuL)₂Mn(nic)(H₂O)]⁺ for 1 and [(CuL)₂Mn(nic)]⁺ for 3, are the active species that bind to the substrate, and on that basis, probable mechanisms through the formation of radical intermediates have been proposed.

Structure of Pb(Fe2/3W1/3)O3 single crystals with partial cation order

Despite intensive studies on the complex perovskite Pb(Fe_2/3W_1/3)O₃ (PFWO) relaxor, understanding the exact nature of its multifunctional properties has remained a challenge for decades. In this work we report a comprehensive structural study of the PFWO single crystals using a combination of synchrotron X-ray diffraction and high-resolution electron microscopy. The set of {h + ½, k + ½, l + ½} superlattice reflections was observed for the first time based on single-crystal synchrotron X-ray experiments (100-450 K) and transmission electron microscopy investigations, which indicates some kind of B-cation ordering in PFWO which had been thought to be totally disordered. It was found that (1) the crystal structure of PFWO should be described by a partly ordered cubic perovskite (i.e. Fm - 3m), (2) the weak ferromagnetic properties and excess magnetic moment of PFWO can be understood based on non-random distribution of Fe cations between the 4a and 4b sites, and (3) the Pb displacement disorder is present in this material and the cations are probably displaced along the <100> directions. The X-ray diffraction results of this investigation show that partial cation ordering indeed exists in PFWO, which makes it necessary to revisit the generally accepted interpretations of the results obtained up to date. In agreement with X-ray diffraction study the main results of TEM study include: (1) a long range order that can be described with the Fm - 3m symmetry is reliably detected, (2) the coherence length of that long range order is in the order of 1-2 nm and (3) no remarkable chemical inhomogeneity is found in the tested PFWO crystal, excluding the possibility of a compositional ordering arising from substitutional defects in the perovskite structure.

Hydrogen and Halogen Bond Mediated Coordination Polymers of Chloro-Substituted Pyrazin-2-Amine Copper(I) Bromide Complexes

A new class of six mono- (1; 3-Cl-, 2; 5-Cl-, 3; 6-Cl-) and di-(4; 3,6-Cl, 5; 5,6-Cl-, 6; 3,5-Cl-) chloro-substituted pyrazin-2-amine ligands (1–6) form complexes with copper (I) bromide, to give 1D and 2D coordination polymers through a combination of halogen and hydrogen bonding that were characterized by X-ray diffraction analysis. These Cu(I) complexes were prepared indirectly from the ligands and CuBr2 via an in situ redox process in moderate to high yields. Four of the pyrazine ligands, 1, 4–6 were found to favor a monodentate mode of coordination to one CuI ion. The absence of a C6-chloro substituent in ligands 1, 2 and 6 supported N1–Cu coordination over the alternative N4–Cu coordination mode evidenced for ligands 4 and 5. These monodentate systems afforded predominantly hydrogen bond (HB) networks containing a catenated (μ3-bromo)-CuI ‘staircase’ motif, with a network of ‘cooperative’ halogen bonds (XB), leading to infinite polymeric structures. Alternatively, ligands 2 and 3 preferred a μ2-N,N’ bridging mode leading to three different polymeric structures. These adopt the (μ3-bromo)-CuI ‘staircase’ motif observed in the monodentate ligands, a unique single (μ2-bromo)-CuI chain, or a discrete Cu2Br2 rhomboid (μ2-bromo)-CuI dimer. Two main HB patterns afforded by self-complimentary dimerization of the amino pyrazines described by the graph set notation R22(8) and non-cyclic intermolecular N–H∙∙∙N’ or N–H∙∙∙Br–Cu leading to infinite polymeric structures are discussed. The cooperative halogen bonding between C–Cl∙∙∙Cl–C and the C–Cl∙∙∙Br–Cu XB contacts are less than the sum of the van der Waals radii of participating atoms, with the latter ranging from 3.4178(14) to 3.582(15) Å. In all cases, the mode of coordination and pyrazine ring substituents affect the pattern of HBs and XBs in these supramolecular structures.

Aspects of lanthanide complexes for selectivity, intensity and sharpness in luminescence bands from twenty-four praseodymium, europium and gadolinium complexes with differently distorted-hexadentate ligands

We structurally and spectroscopically investigated a series of praseodymium (Pr) complexes with eight ligands that form helicate molecular structures. The mother ligand skeleton (L) has two bipyridine moieties bridged with ethylenediamine. The bridged skeleton of PrL was changed to diamines 1-methyl-ethylenediamine, trimethylenediamine and 2,2'-dimethyl-trimethylenediamine, and the corresponding ligands were designated as L^me, L^pr and L^dmpr, for each Pr in these complexes upon UV-excitation. The luminescence quantum yields of PrL and PrL^pr in the visible and near infrared (NIR) regions indicate that PrL is excited by both the electronic state of the ligand and the ff absorption band, whereas PrL^pr is excited through the ligand. The addition of a methyl group to PrL and PrL^pr has a different effect on the Pr emission intensity with the intensity of PrL^me decreasing more than that of PrL and PrL^dmpr and increasing more than that of PrL^pr. Thus, the coordination of Pr and the increased rigidity of the ligand upon methylation enhance luminescence. The azomethine moieties on L^me, L^pr and L^dmpr were reduced and formed the corresponding PrLH, PrL^meH, PrL^prH and PrL^dmprH complexes. The luminescence of the non-methylated series is due to transitions related to the ¹D₂ level and thus the methylated series luminesces due to high energy levels such as ³P_J arising from the shortened π electronic systems. We also discuss the strong red emission of a series of Eu complexes with eight ligands from the viewpoint of their molecular structures and luminescence efficiencies and evaluate the Judd-Ofelt parameters from the luminescence spectra of Eu complexes.

Opportunities and challenges in neutron crystallography

Neutron and X-ray crystallography are complementary to each other. While X-ray scattering is directly proportional to the number of electrons of an atom, neutrons interact with the atomic nuclei themselves. Neutron crystallography therefore provides an excellent alternative in determining the positions of hydrogens in a biological molecule. In particular, since highly polarized hydrogen atoms (H+) do not have electrons, they cannot be observed by X-rays. Neutron crystallography has its own limitations, mainly due to inherent low flux of neutrons sources, and as a consequence, the need for much larger crystals and for different data collection and analysis strategies. These technical challenges can however be overcome to yield crucial structural insights about protonation states in enzyme catalysis, ligand recognition, as well as the presence of unusual hydrogen bonds in proteins.

Interactive model building in neutron macromolecular crystallography

This chapter aims to give an overview of the process of interactive model building in macromolecular neutron crystallography for the researcher transitioning from X-ray crystallography alone. The two most popular programs for refinement and model building, phenix.refine and Coot, respectively, are used as examples, and familiarity with the programs is assumed. Some work-arounds currently required for proper communication between the programs are described. We also discuss the appearance of nuclear density maps and how this differs from that of electron density maps. Advice is given to facilitate deposition of jointly refined neutron/X-ray structures in the Protein Data Bank.

Dynamic nuclear polarization enhanced neutron crystallography: Amplifying hydrogen in biological crystals

Dynamic nuclear polarization (DNP) can provide a powerful means to amplify neutron diffraction from biological crystals by 10-100-fold, while simultaneously enhancing the visibility of hydrogen by an order of magnitude. Polarizing the neutron beam and aligning the proton spins in a polarized sample modulates the coherent and incoherent neutron scattering cross-sections of hydrogen, in ideal cases amplifying the coherent scattering by almost an order of magnitude and suppressing the incoherent background to zero. This chapter describes current efforts to develop and apply DNP techniques for spin polarized neutron protein crystallography, highlighting concepts, experimental design, labeling strategies and recent results, as well as considering new strategies for data collection and analysis that these techniques could enable.

What are the current limits on determination of protonation state using neutron macromolecular crystallography?

The rate of deposition of models determined by neutron diffraction, or a hybrid approach that combines X-ray and neutron diffraction, has increased in recent years. The benefit of neutron diffraction is that hydrogen atom (H) positions are detectable, allowing for the determination of protonation state and water molecule orientation. This study analyses all neutron models deposited in the Protein Data Bank to date, focusing on protonation state and properties of H (or deuterium, D) atoms as well as the details of water molecules. In particular, clashes and hydrogen bonds involving H or D atoms are investigated. As water molecules are typically the least reproducible part of a structural model, their positions in neutron models were compared to those in homologous high-resolution X-ray structures. For models determined by joint refinement against X-ray and neutron data, the water structure comparison was also carried out for models re-refined against the X-ray data alone. The homologues have generally fewer conserved water molecules where X-ray only was used and the positions of equivalent waters vary more than in the case of the hybrid X-ray model. As neutron diffraction data are generally less complete than X-ray data, the influence of neutron data completeness on nuclear density maps was also analyzed. We observe and discuss systematic map quality deterioration as result of data incompleteness.

Fundamentals of neutron crystallography in structural biology

This chapter introduces this topic for the whole volume. It is not a review, rather it presents the basics, the key considerations and forward references to the other chapters. This starts by setting the scene of principles and overall strategy, moves onto planning an experiment including its feasibility and then outlines practicalities with options for the experiment. The crystal structure that results will lead to publication and associated with it, Protein Data Bank deposition.

Facile synthesis of a new Cu(ii) complex with an unsymmetrical ligand and its use as an O3 donor metalloligand in the synthesis of Cu(ii)-Mn(ii) complexes: structures, magnetic properties, and catalytic oxidase activities

A new, facile Cu(ii) template method has been employed for the unsymmetrical dicondensation of 1,2-ethylenediamine with salicylaldehyde and o-vanillin. The mononuclear complex, [CuL] (1), thus obtained, has been used as an O₃ donor metalloligand for the synthesis of four new Cu(ii)-Mn(ii) complexes, [(CuL)MnCl₂] (2), [(CuL)Mn(NO₃)₂(CH₃OH)]_n (3), {[(CuL)Mn(benz)(H₂O)]₂·(CuL)₂(ClO₄)₂} (4) and [(CuL)Mn(benz)Cl]₂ (5) (where benz = benzoate). Single-crystal structural analyses reveal that 2 is a dinuclear complex while complex 3 is polymeric with a repeating dinuclear [(CuL)Mn(NO₃)₂(CH₃OH)] unit, linked via the nitrate ion. Both 4 and 5 are discrete tetranuclear complexes, where the dinuclear units [(CuL)Mn(benz)(H₂O)] and [(CuL)Mn(benz)Cl] are connected by double benzoate and double chloride bridges, respectively. In complex 4, two monomeric [CuL] units are cocrystallized with the tetranuclear complex. An important difference in the structure of 4 from the other three complexes is that one solvent water molecule is coordinated to each Mn(ii) ion, which makes complex 4 catalytically very active towards mimicking catecholase and phenoxazinone synthase-like oxidation reactions. The turnover numbers (k_cat) for the aerial oxidation of 3,5-di-tert-butylcatechol and o-aminophenol are 399 h^-1 and 230 h^-1, respectively. The evidence of the intermediate species in the mass spectra indicates possible heterometallic cooperation where the Mn(ii) center helps in substrate binding and Cu(ii) participates in the oxidation reactions with molecular oxygen. Cyclic voltammetry measurements suggest the reduction of Cu(ii) to Cu(i) during the catalytic process. Temperature-dependent dc molar magnetic susceptibility measurements reveal that complexes 2-5 are antiferromagnetically coupled with the exchange coupling constants (J) of J = -13.5 cm^-1 and J = -13.5 cm^-1 for 2 and 3, respectively, J₁ = -12.6 cm^-1 and J₂ = -1.20 cm^-1 for complex 4 and J₁ = -13.24 cm^-1 and J₂ = 0.36 cm^-1 for complex 5 as is expected from the Cu-O-Mn bridging angles.

One- and Two-Component Organogels Containing Cyanostilbene without any Auxiliary Substituents

Pyridyl acrylonitrile without traditional auxiliary groups form stable organogels in ethanol. The addition of a second non-gelating cyanostilbene component results in a more stable two-component gel. Single crystal X-ray data reveal the influence of C-H⋅ ⋅ ⋅N, C-H⋅ ⋅ ⋅π, and π-π interactions in the formation of organogels. The morphology of the xerogels was studied by using SEM, which showed the self-assembly of molecules to fibers and sheet-like structures, and phase differences upon the gel formation and the structural phase characterization was measured using powder XRD. Exposure of the organogels to acidic (TFA) vapors results in distinct color changes and loss of gelation properties, thus highlighting the potential of these gels in sensing. The results represent a rare example of two-component organogels using two different cyanostilbene units and show that functional two-component organogels can be formed by utilizing the synergistic effects of the individual components.

Topotactic desolvation and condensation reactions of 3D Zn3TiF7(H2O)2(taz)3·S (S = 3H2O or C2H5OH)

Thermodiffraction, IR, DFT calculations, and ¹H and ¹⁹F NMR characterizations of the desolvatation and reversible condensation reactions of Zn₃TiF₇(taz)₃ family.

Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix

A fundamental prerequisite for implementing new procedures of atomic model refinement against neutron diffraction data is the efficient handling of hydrogen atoms. The riding hydrogen model, which constrains hydrogen atom parameters to those of the non-hydrogen atoms, is a plausible parameterization for refinements. This work describes the implementation of the riding hydrogen model in the Computational Crystallography Toolbox and in Phenix. Riding hydrogen atoms can be found in several different configurations that are characterized by specific geometries. For each configuration, the hydrogen atom parameterization and the expressions for the gradients of refinement target function with respect to non-hydrogen parameters are described.

Combined experimental and theoretical studies on a phenyl thiadiazole-based novel turn-on fluorescent colorimetric Schiff base chemosensor for the selective and sensitive detection of Al3+

A phenyl thiadiazole based receptor (L) has been presented for fluorescent colorimetric detection of Al³⁺ ion with very low detection limit in aqueous medium. The probe L can be applied for logic gate formation, recovery of contaminated water samples and smart-phone based analysis.