Diverse Co(II) Coordination Polymers with the Same Mixed Ligands: Evaluation of Chemical Stability and Structural Transformation.

Reactions of Co(OAc)2·4H2O, N'N'-bis(3-pyridylmethyl)oxalamide (L) and 4,4'-sulfonyldibenzoic acid (H2SDA) afforded four coordination polymers with the same mixed ligands, {[Co(L)(SDA)(H2O)2]·H2O·CH3OH}n, 1, {[Co(L)0.5(SDA)]·2H2O·0.5L}n, 2, {[Co(L)1.5(SDA)(H2O)]·H2O}n, 3, and {[Co2(L)1.5(SDA)2(H2O)2]·4H2O}n, 4, which have been structurally characterized using single-crystal X-ray crystallography. Complexes 1-4 are 2D layers, revealing topologies of sql, 2,6L1, (4,4)Ia, and 6L12, respectively, and demonstrating that the metal-to-ligand ratio, solvent system, and reaction temperature are important in determining the structural diversity. The immersion of these complexes into various solvents shows that the structural types govern the chemical stabilities of 1-4. Reversible structural transformation is shown for complexes 1 and 2 upon solvent removal and adsorption, while those of 3 and 4 are irreversible.

Synthesis and Structure of Protonated Sulfur Dioxide.

Salts of protonated sulfur dioxide were synthesized by recrystallization of [FS(OX)2][SbF6] (X=H, D) in aprotic solvents at low temperatures. Hemiprotonated sulfur dioxide [(SO2)2H][Sb2F11] was obtained from the solvent SO2 and the monoprotonated sulfur dioxide [OSOD][Sb2F11], using 1,1,1,2-tetrafluoroethane as solvent. For both compounds, single crystals were obtained and an X-ray structure analysis was conducted. Furthermore, the salts were characterized by Raman spectroscopy and the results were discussed together with quantum chemical calculations on the M06-2X/aug-cc-pVTZ level of theory.

Growth-Coupled Evolutionary Pressure Improving Epimerases for D-Allulose Biosynthesis Using a Biosensor-Assisted In Vivo Selection Platform.

Fast screening strategies that enable high-throughput evaluation and identification of desired variants from diversified enzyme libraries are crucial to tailoring biocatalysts for the synthesis of D-allulose, which is currently limited by the poor catalytic performance of ketose 3-epimerases (KEases). Here, the study designs a minimally equipment-dependent, high-throughput, and growth-coupled in vivo screening platform founded on a redesigned D-allulose-dependent biosensor system. The genetic elements modulating regulator PsiR expression levels undergo systematic optimization to improve the growth-responsive dynamic range of the biosensor, which presents ≈30-fold facilitated growth optical density with a high signal-to-noise ratio (1.52 to 0.05) toward D-allulose concentrations from 0 to 100 mm. Structural analysis and evolutionary conservation analysis of Agrobacterium sp. SUL3 D-allulose 3-epimerase (ADAE) reveal a highly conserved catalytic active site and variable hydrophobic pocket, which together regulate substrate recognition. Structure-guided rational design and directed evolution are implemented using the growth-coupled in vivo screening platform to reprogram ADAE, in which a mutant M42 (P38N/V102A/Y201L/S207N/I251R) is identified with a 6.28-fold enhancement of catalytic activity and significantly improved thermostability with a 2.5-fold increase of the half-life at 60 °C. The research demonstrates that biosensor-assisted growth-coupled evolutionary pressure combined with structure-guided rational design provides a universal route for engineering KEases.

Fragment-Based Design, Synthesis, and Characterization of Aminoisoindole-Derived Furin Inhibitors.

A 1H-isoindol-3-amine was identified as suitable P1 group for the proprotein convertase furin using a crystallographic screening with a set of 20 fragments known to occupy the S1 pocket of trypsin-like serine proteases. Its binding mode is very similar to that observed for the P1 group of benzamidine-derived peptidic furin inhibitors suggesting an aminomethyl substitution of this fragment to obtain a couplable P1 residue for the synthesis of substrate-analogue furin inhibitors. The obtained inhibitors possess a slightly improved picomolar inhibitory potency compared to their benzamidine-derived analogues. The crystal structures of two inhibitors in complex with furin revealed that the new P1 group is perfectly suited for incorporation in peptidic furin inhibitors. Selected inhibitors were tested for antiviral activity against respiratory syncytial virus (RSV) and a furin-dependent influenza A virus (SC35M/H7N7) in A549 human lung cells and demonstrated an efficient inhibition of virus activation and replication at low micromolar or even submicromolar concentrations. First results suggest that the Mas-related G-protein coupled receptor GPCR-X2 could be a potential off-target for certain benzamidine-derived furin inhibitors.

Dual Engineering of Olivetolic Acid Cyclase and Tetraketide Synthase for the Formation of Longer Alkyl-Chain Olivetolic Acid Analogs and Their Antibacterial Activities.

Among presently used pharmaceuticals, about 60% were developed from natural products with unique chemical diversity and biological activities. Hence, the discovery of new bioactive compounds from natural products is still important for further drug development. In addition, breakthroughs in synthetic biology have also begun to produce many useful compounds through manipulations of the biosynthetic genes for secondary metabolites. Theoretically, this approach can also be exploited to generate new unnatural compounds by intermixing the genes from different biosynthetic pathways and/or engineering the secondary metabolite enzyme(s) with expanded substrate and product specificities. Δ9-Tetrahydrocannabinol (Δ9-THC), the heat-decarboxylated tetrahydrocannabinolic acid (Δ9-THCA) produced by Cannabis sativa, is the most important therapeutic cannabinoid due to its useful pharmacological features, such as analgesic, anti-emetic, anti-inflammatory, and anti-epileptic activities. In the structures of cannabinoids, the resorcinyl alkyl chain is a critical pharmacophore, and the therapeutic effects of Δ9-THC can be enhanced by converting the pentyl (C5) moiety at C-3 to other acyl moieties. Thus, the expansion of unnatural cannabinoids with different C-3 alkyl moiety analogs might establish an excellent platform for the further development of therapeutically beneficial cannabinoids. This article reviews the structure-based dual engineering of both enzymes responsible for the formation of the resorcinyl core of Δ9-THC and describes the effect of C-6 alkyl-length extension of olivetolic acid, along with related analogs, on the antibacterial activities against Bacillus subtilis and Staphylococcus aureus.

Cu(II) Coordination Polymers Containing Mixed Ligands with Different Flexibilities: Structural Diversity and Iodine Adsorption.

Reactions of N,N'-bis(3-methylpyridyl)oxalamide (L1), N,N'-bis(3-methylpyridyl)adipoamide (L2) and N,N'-bis(3-methylpyridyl)sebacoamide (L3) with tricarboxylic acids and Cu(II) salts afforded {[Cu(L1)(1,3,5-HBTC)]·H2O}n (1,3,5-H3BTC = 1,3,5-benzenetricarboxylic acid), 1, {[Cu1.5(L2)1.5(1,3,5-BTC)(H2O)2]·6.5H2O}n, 2, [Cu(L2)0.5(1,3,5-HBTB)]n (1,3,5-H3BTB = 1,3,5-tri(4-carboxyphenyl)benzene), 3, [Cu4(L3)(OH)2(1,3,5-BTC)2]n, 4, {[Cu3(L3)2(1,3,5-BTB)2]·2.5MeOH·2H2O}n, 5, and {[Cu3(L3)2(1,3,5-BTB)2 ]·DMF·2H2O}n, 6, which have been structurally characterized by using single crystal X-ray crystallography. Complexes 1-4 form a 2D layer with the {44.62}-sql topology, a 2D layer with the (4.62)2(42.62.82)-bex topology, a three-fold interpenetrated 3D net with the (412·63)-pcu topology and a 3D framework with the (410·632·83)(42·6)2(43·63) topology, respectively, whereas 5 and 6 are 3D frameworks with the (63)2(64·82)(68·85·102) topology. Complex 5 shows a better iodine adsorption factor of 290.0 mg g-1 at 60 °C for 360 min than the other ones, revealing that the flexibility of the spacer ligand governs the structural diversity and the adsorption capacity.

Algorithms for magnetic symmetry operation search and identification of magnetic space group from magnetic crystal structure.

A crystal symmetry search is crucial for computational crystallography and materials science. Although algorithms and implementations for the crystal symmetry search have been developed, their extension to magnetic space groups (MSGs) remains limited. In this paper, algorithms for determining magnetic symmetry operations of magnetic crystal structures, identifying magnetic space-group types of given MSGs, searching for transformations to a Belov-Neronova-Smirnova (BNS) setting, and symmetrizing the magnetic crystal structures using the MSGs are presented. The determination of magnetic symmetry operations is numerically stable and is implemented with minimal modifications from the existing crystal symmetry search. Magnetic space-group types and transformations to the BNS setting are identified by a two-step approach combining space-group-type identification and the use of affine normalizers. Point coordinates and magnetic moments of the magnetic crystal structures are symmetrized by projection operators for the MSGs. An implementation is distributed with a permissive free software license in spglib v2.0.2: https://github.com/spglib/spglib.

In-silico investigation of 4-nitro-N-1H-pyrazol-3-ylbenzamide towards its potential use against SARS-CoV-2: a DFT, molecular docking and molecular dynamics study.

In the present research work, we report the synthesis and characterization of novel pyrazole derivative obtained by the condensation reaction of 4-nitro benzaldehyde group with one equivalent of the 2-amino pyrazole yielding 4-nitro-N-1H-pyrazol-3-ylbenzamide with high yield. The two symmetry-independent molecules (molecule A and molecule B) differ about the central C-N bond, with the dihedral angles between the pyrazole ring system and the nitrobenzene ring being 13.90° and 18.64°, respectively. By optimizing the symmetry-independent dimer molecules, the rotational barrier between the conformers is found to be within the 2.5-5.5 kcal/mol range. QTAIM and RDG based NCI isosurface revealed the presence of strong N-H…N and C-H…O hydrogen bonds which stabilize the two independent centrosymmetric inversion-related dimers. Further, weak and short directional interactions such as C-H…N, H…H and C-H…π were also analyzed systematically using various topological parameters. The compound is found to adhere to the Lipinski's rule of five and exhibit good pharmacokinetic properties. The results of molecular docking studies performed against SARS-CoV-2 virus main protease (PDB IDs: 6LU7, 6W9C and 6WQF) revealed that the compound showed better docking scores. Molecular docking studies verified the inhibition activity of the synthesized novel compound. Finally, the binding free energy and contributed energies were calculated using MM-GBSA method. The 6LU7-ligand complex showed highest binding free energy and among all other interactions, the contributions of the covalent binding and van der Waals energy are found to be significant.Communicated by Ramaswamy H. Sarma.

The Crucial Role of Sb2 F10 in the Chemical Synthesis of F2.

The purely chemical synthesis of fluorine is a spectacular reaction which for more than a century had been believed to be impossible. In 1986, it was finally experimentally achieved, but since then this important reaction has not been further studied and its detailed mechanism had been a mystery. The known thermal stability of MnF4 casts serious doubts on the originally proposed hypothesis that MnF4 is thermodynamically unstable and decomposes spontaneously to a lower manganese fluoride and F2 . This apparent discrepancy has now been resolved experimentally and by electronic structure calculations. It is shown that the reductive elimination of F2 requires a large excess of SbF5 and occurs in the last reaction step when in the intermediate [SbF6 ][MnF2 ][Sb2 F11 ] the addition of one more SbF5 molecule to the [SbF6 ]- anion generates a second tridentate [Sb2 F11 ]- anion. The two tridentate [Sb2 F11 ]- anions then provide six fluorine bridges to the Mn atom thereby facilitating the reductive elimination of the two fluorine ligands as F2 .

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles.

Proteins are dynamic macromolecules that perform vital functions in cells. A protein structure determines its function, but this structure is not static, as proteins change their conformation to achieve various functions. Understanding the conformational landscapes of proteins is essential to understand their mechanism of action. Sets of carefully chosen conformations can summarize such complex landscapes and provide better insights into protein function than single conformations. We refer to these sets as representative conformational ensembles. Recent advances in computational methods have led to an increase in the number of available structural datasets spanning conformational landscapes. However, extracting representative conformational ensembles from such datasets is not an easy task and many methods have been developed to tackle it. Our new approach, EnGens (short for ensemble generation), collects these methods into a unified framework for generating and analyzing representative protein conformational ensembles. In this work, we: (1) provide an overview of existing methods and tools for representative protein structural ensemble generation and analysis; (2) unify existing approaches in an open-source Python package, and a portable Docker image, providing interactive visualizations within a Jupyter Notebook pipeline; (3) test our pipeline on a few canonical examples from the literature. Representative ensembles produced by EnGens can be used for many downstream tasks such as protein-ligand ensemble docking, Markov state modeling of protein dynamics and analysis of the effect of single-point mutations.

The mitochondrial intermembrane space protein mitofissin drives mitochondrial fission required for mitophagy.

Mitophagy plays an important role in mitochondrial homeostasis by selective degradation of mitochondria. During mitophagy, mitochondria should be fragmented to allow engulfment within autophagosomes, whose capacity is exceeded by the typical mitochondria mass. However, the known mitochondrial fission factors, dynamin-related proteins Dnm1 in yeasts and DNM1L/Drp1 in mammals, are dispensable for mitophagy. Here, we identify Atg44 as a mitochondrial fission factor that is essential for mitophagy in yeasts, and we therefore term Atg44 and its orthologous proteins mitofissin. In mitofissin-deficient cells, a part of the mitochondria is recognized by the mitophagy machinery as cargo but cannot be enwrapped by the autophagosome precursor, the phagophore, due to a lack of mitochondrial fission. Furthermore, we show that mitofissin directly binds to lipid membranes and brings about lipid membrane fragility to facilitate membrane fission. Taken together, we propose that mitofissin acts directly on lipid membranes to drive mitochondrial fission required for mitophagy.

The polymorph landscape of dabigatran etexilate mesylate: Taking the challenge to bring a metastable polymorph to market.

Dabigatran etexilate mesylate is polymorphic and can exist in different crystalline forms. Two polymorphs have been encountered during the development of this drug substance, namely anhydrous form I and anhydrous form II. Additionally, a hemihydrate was observed, if larger amounts of water were present during crystallization in the salt formation step. Finally, a high temperature form III can be obtained by heating anhydrous form I above 150 °C. All three at room-temperature accessible forms were characterized by means of microscopy, X-ray powder diffraction, thermal analysis, IR- and Raman spectroscopy. In addition, solubility parameters (equilibrium solubility and intrinsic dissolution rate, heat of solution) were collected on all three forms. The crystal structure of all three at room-temperature accessible forms could be obtained using electron diffraction. Anhydrous form I has a monoclinic crystal lattice (C2/c), anhydrous form II a triclinic one (P1¯), and the hemihydrate crystallizes also in a monoclinic space group (P2/c). From the obtained data there is clear evidence that anhydrous form II is thermodynamically more stable than anhydrous form I. Form I and form II are monotropically related to each other indicating that they may coexist over a wide temperature range. The hemihydrate is a completely independent crystalline modification of dabigatran etexilate mesylate. It is another thermodynamically stable form and structurally not related to the two anhydrous forms. The hemihydrate melts at ca. 125 °C, there is no conversion to either anhydrous form I or form II upon dehydration. The high temperature form III is enantiotropically related to form I and only stable above the phase transition temperature at ca. 150 °C and its melting point at ca. 183 °C. The energy difference between anhydrous form I and form II was found to be only 2.5 - 3.0 J/g. Both forms have very similar aqueous solubility characteristics. Although anhydrous form II is the thermodynamically more stable form, anhydrous form I was chosen for development. The selection of form I for development was mainly based on the superior bulk processing properties of anhydrous form I in drug substance synthesis and further drug product processing as well as its slightly better chemically stability in pivotal long term stability studies. Anhydrous form I, although meta stable, is still stable enough that conversion to the more stable form II can occur only to a limited extent during drug substance synthesis and drug product manufacturing. From long term stability data on both bulk drug substance as well as drug product, there is no indication that form I transforms to form II during storage. Even under stress conditions where form I was stored up to 4 weeks at 70 °C, no conversion to form II was observed.

A general force field by machine learning on experimental crystal structures. Calculations of intermolecular Gibbs energy with FlexCryst.

Machine learning was employed on the experimental crystal structures of the Cambridge Structural Database (CSD) to derive an intermolecular force field for all available types of atoms (general force field). The obtained pairwise interatomic potentials of the general force field allow for the fast and accurate calculation of intermolecular Gibbs energy. The approach is based on three postulates regarding Gibbs energy: the lattice energy must be below zero, the crystal structure must be a local minimum, and, if available, the experimental and the calculated lattice energy must coincide. The parametrized general force field was then validated regarding these three conditions. First, the experimental lattice energy was compared with the calculated energies. The observed errors were found to be in the order of experimental errors. Second, Gibbs lattice energy was calculated for all structures available in the CSD. Their energy values were found to be below zero in 99.86% of the cases. Finally, 500 random structures were minimized, and the change in density and energy was examined. The mean error in the case of density was below 4.06%, and for energy it was below 5.7%. The obtained general force field calculated Gibbs lattice energies of 259 041 known crystal structures within a few hours. Since Gibbs energy defines the reaction energy, the calculated energy can be used to predict chemical-physical properties of crystals, for instance, the formation of co-crystals, polymorph stability and solubility.

Metal and Ligand Effect on the Structural Diversity of Divalent Coordination Polymers with Mixed Ligands: Evaluation for Photodegradation.

Eight coordination polymers constructed from divalent metal salts, N,N'-bis(pyridin-3-ylmethyl)terephthalamide (L), and various dicarboxylic acids are reported, affording [Co(L)(5-ter-IPA)(H2O)2]n (5-tert-H2IPA = 5-tert-butylisophthalic acid), 1, {[Co(L)(5-NO2-IPA)]⋅2H2O}n (5-NO2-H2IPA = 5-nitroisophthalic acid), 2, {[Co(L)0.5(5-NH2-IPA)]⋅MeOH}n (5-NH2-H2IPA = 5-aminoisophthalic acid), 3, {[Co(L)(MBA)]⋅2H2O}n (H2MBA = diphenylmethane-4,4'-dicarboxylic acid), 4, {[Co(L)(SDA)]⋅H2O}n (H2SDA = 4,4-sulfonyldibenzoic acid), 5, {[Co2(L)2(1,4-NDC)2(H2O)2]⋅5H2O}n (1,4-H2NDC = naphthalene-1,4-dicarboxylic acid), 6, {[Cd(L)(1,4-NDC)(H2O)]⋅2H2O}n, 7, and {[Zn2(L)2(1,4-NDC)2]⋅2H2O}n, 8, which were structurally characterized by using single-crystal X-ray diffraction. The structural types of 1-8 are subject to the metal and ligand identities, showing a 2D layer with the hcb, a 3D framework with the pcu, a 2D layer with the sql, a polycatenation of 2-fold interpenetrated 2D layer with the sql, a 2-fold interpenetrated 2D layer with the 2,6L1, a 3D framework with the cds, a 2D layer with the 2,4L1, and a 2D layer with the (102⋅12)(10)2(4⋅10⋅124)(4) topologies, respectively. The investigation on the photodegradation of methylene blue (MB) by using complexes 1-3 reveals that the degradation efficiency may increase with increasing surface areas.

Structural Insights into Layered Tetrahalocuprates(II) Based on Small Unsaturated and Cyclic Primary Ammonium Cations.

Layered hybrid halometallates represent a promising class of multifunctional materials, yet with many open challenges regarding the interaction between building blocks. In this work, we present a synthetic and analytical methodology for the efficient synthesis and structural analysis of a series of novel tetrahalocuprate(II) hybrids based on small alkylammonium cations. Observed robustness in geometrical motifs provided a platform for crystal structure determination, even from the complex laboratory powder diffraction data. The slight differences in inorganic layer geometry and severe differences in organic bilayer packing are quantified using well-established descriptors for these materials, and dependences of geometric parameters on anion and cation choice are accounted for. Temperature dependence of structural parameters for one of the tetrachlorocuprate hybrids that was chosen as a model unveils a possible geometrical origin of thermochromism in these materials.

Polyaromatic Group Embedded Cd(II)-Coordination Polymers for Microwave-Assisted Solvent-Free Strecker-Type Cyanation of Acetals.

In this work, two new 1D Cd(II) coordination polymers (CPs), [Cd(L1)(NMF)2]n (1) and [Cd(L2)(DMF)(H2O)2]n·n(H2O) (2), have been synthesized, characterized and employed as catalysts for the microwave-assisted solvent-free Strecker-type cyanation of different acetals. Solvothermal reaction between the pro-ligand, 5-{(pyren-1-ylmethyl)amino}isophthalic acid (H2L1) or 5-{(anthracen-9-ylmethyl)amino}isophthalic acid (H2L2), and Cd(NO3)2.6H2O in the presence of NMF or DMF:THF solvent, produces the coordination polymer 1 or 2, respectively. These frameworks were characterized by single-crystal and powder X-ray diffraction analyses, ATR-FTIR, elemental and thermogravimetry analysis. Their structural analysis revealed that both CPs show one-dimensional structures, but CP 1 has a 1D double chain type structure whereas CP 2 is a simple one-dimensional network. In CP 1, the dinuclear {Cd2(COO)4} unit acts as a secondary building unit (SBU) and the assembly of dinuclear SBUs with deprotonated ligand (L12-) led to the formation of a 1D double chain framework. In contrast, no SBU was observed in CP 2. To test the catalytic effectiveness of these 1D compounds, the solvent-free Strecker-type cyanation reactions of different acetals in presence of trimethylsilyl cyanide (TMSCN) was studied with CPs 1 and 2 as heterogenous catalysts. CP 1 displays a higher activity (yield 95%) compared to CP 2 (yield 84%) after the same reaction time. This is accounted for by the strong hydrogen bonding packing network in CP 2 that hampers the accessibility of the metal centers, and the presence of the dinuclear Cd(II) SBU in CP 1 which can promote the catalytic process in comparison with the mononuclear Cd(II) center in CP 2. Moreover, the recyclability and heterogeneity of both CPs were tested, demonstrating that they can be recyclable for at least for four cycles without losing their structural integrity and catalytic activity.

New Organic-Inorganic Hybrid Compounds Based on Sodium Peroxidomolybdates (VI) and Derivatives of Pyridine Acids: Structure Determination and Catalytic Properties.

Two organic-inorganic hybrids based on sodium peroxidomolybdates(VI) and 3,5-dicarboxylic pyridine acid (Na-35dcpa) or N-oxide isonicotinic acid (Na-isoO) have been synthesized and characterized. All compounds contain inorganic parts: a pentagonal bipyramid with molybdenum center, and an organic part containing 3,5-dicarboxylic pyridine acid or N-oxide isonicotinic acid moieties. The type of organic part used in the synthesis influences the crystal structure of obtained compounds. This aspect can be interesting for crystal engineering. Crystal structures were determined using powder X-ray diffraction or single crystal diffraction for compounds Na-35dcpa and Na-isoO, respectively. Elemental analysis was used to check the purity of the obtained compounds, while X-ray Powder Diffraction (XRPD) vs. temp. was applied to verify their stability. Moreover, all the compounds were examined by Infrared (IR) spectroscopy. Their catalytic activity was tested in the Baeyer-Villiger (BV) oxidation of cyclohexanone to ε-caprolactone in the oxygen-aldehyde system. The highest catalytic activity in the BV oxidation was observed for Na-35dcpa. The compounds were also tested for biological activity on human normal cells (fibroblasts) and colon cancer cell lines (HT-29, LoVo, SW 620, HCT 116). All compounds were cytotoxic against tumor cells with metastatic characteristics, which makes them interesting and promising candidates for further investigations of specific anticancer mechanisms.

Structural Diversity of Mercury(II) Halide Complexes Containing Bis-pyridyl-bis-amide with Bulky and Angular Backbones: Ligand Effect and Metal Sensing.

Hg(II) halide complexes [HgCl2] 2L1 [L1 = N,N'-bis(3-pyridyl)bicyclo(2,2,2,)oct-7-ene-2,3,5,6-tetracarboxylic diamide), 1, [HgBr2(L1)]n, 2, [HgI2(L1)], 3, [Hg2X4(L2)2] [X = Cl, 4, Br, 5, and I, 6; L2 = N,N'-bis(4-pyridylmethyl)bicyclo(2,2,2,)oct-7-ene-2,3,5,6-tetracarboxylic diamide] and {[HgX2(L3)]⋅H2O}n [X = Cl, 7, Br, 8 and I, 9; L3 = 4,4'-oxybis(N-(pyridine-3-yl)benzamide)] are reported and structurally characterized using single-crystal X-ray diffraction analyses. The linear HgCl2 units of complex 1 are interlinked by the L1 ligands through Hg---N and Hg---O interactions, resulting in 1D supramolecular chains. Complex 2 shows 1D zigzag chains interlinked through the Br---Br interactions to form 1D looped supramolecular chains, while the mononuclear [HgI2L2] molecules of 3 are interlinked through Hg---O and I---I interactions, forming 2D supramolecular layers. Complexes 4-6 are isomorphous dinuclear metallocycles, and 7-9 form isomorphous 1D zigzag chains. The roles of the ligand type and the halide anion in determining the structural diversity of 1-9 is discussed and the luminescent properties of 7-9 evaluated. Complexes 7-9 manifest stability in aqueous environments. Moreover, complexes 7 and 8 show good sensing towards Fe3+ ions with low detection limits and good reusability up to five cycles, revealing that the Hg-X---Fe3+ (X = Cl and Br) interaction may have an important role in determining the quenching effect of 7 and 8.

The Pnictogen Bond: The Covalently Bound Arsenic Atom in Molecular Entities in Crystals as a Pnictogen Bond Donor.

In chemical systems, the arsenic-centered pnictogen bond, or simply the arsenic bond, occurs when there is evidence of a net attractive interaction between the electrophilic region associated with a covalently or coordinately bound arsenic atom in a molecular entity and a nucleophile in another or the same molecular entity. It is the third member of the family of pnictogen bonds formed by the third atom of the pnictogen family, Group 15 of the periodic table, and is an inter- or intramolecular noncovalent interaction. In this overview, we present several illustrative crystal structures deposited into the Cambridge Structure Database (CSD) and the Inorganic Chemistry Structural Database (ICSD) during the last and current centuries to demonstrate that the arsenic atom in molecular entities has a significant ability to act as an electrophilic agent to make an attractive engagement with nucleophiles when in close vicinity, thereby forming σ-hole or π-hole interactions, and hence driving (in part, at least) the overall stability of the system's crystalline phase. This overview does not include results from theoretical simulations reported by others as none of them address the signatory details of As-centered pnictogen bonds. Rather, we aimed at highlighting the interaction modes of arsenic-centered σ- and π-holes in the rationale design of crystal lattices to demonstrate that such interactions are abundant in crystalline materials, but care has to be taken to identify them as is usually done with the much more widely known noncovalent interactions in chemical systems, halogen bonding and hydrogen bonding. We also demonstrate that As-centered pnictogen bonds are usually accompanied by other primary and secondary interactions, which reinforce their occurrence and strength in most of the crystal structures illustrated. A statistical analysis of structures deposited into the CSD was performed for each interaction type As···D (D = N, O, S, Se, Te, F, Cl, Br, I, arene's π system), thus providing insight into the typical nature of As···D interaction distances and ∠R-As···D bond angles of these interactions in crystals, where R is the remainder of the molecular entity.

AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.

Recent advances in molecular modeling using deep learning have the potential to revolutionize the field of structural biology. In particular, AlphaFold has been observed to provide models of protein structures with accuracies rivaling medium-resolution X-ray crystal structures, and with excellent atomic coordinate matches to experimental protein NMR and cryo-electron microscopy structures. Here we assess the hypothesis that AlphaFold models of small, relatively rigid proteins have accuracies (based on comparison against experimental data) similar to experimental solution NMR structures. We selected six representative small proteins with structures determined by both NMR and X-ray crystallography, and modeled each of them using AlphaFold. Using several structure validation tools integrated under the Protein Structure Validation Software suite (PSVS), we then assessed how well these models fit to experimental NMR data, including NOESY peak lists (RPF-DP scores), comparisons between predicted rigidity and chemical shift data (ANSURR scores), and 15N-1H residual dipolar coupling data (RDC Q factors) analyzed by software tools integrated in the PSVS suite. Remarkably, the fits to NMR data for the protein structure models predicted with AlphaFold are generally similar, or better, than for the corresponding experimental NMR or X-ray crystal structures. Similar conclusions were reached in comparing AlphaFold2 predictions and NMR structures for three targets from the Critical Assessment of Protein Structure Prediction (CASP). These results contradict the widely held misperception that AlphaFold cannot accurately model solution NMR structures. They also document the value of PSVS for model vs. data assessment of protein NMR structures, and the potential for using AlphaFold models for guiding analysis of experimental NMR data and more generally in structural biology.