Quantifying Possible Routes for SpnF-Catalyzed Formal Diels-Alder Cycloaddition.

The Diels-Alder reaction is a cornerstone of modern organic synthesis. Despite this, it remains essentially inaccessible to biosynthetic approaches. Only a few natural enzymes catalyze even a formal [4 + 2] cycloaddition, and it remains uncertain if any of them proceed via the Diels-Alder mechanism. In this study, we focus on the [4 + 2] cycloaddition step in the biosynthesis of spinosyn A, a reaction catalyzed by SpnF enzyme, one of the most promising "true Diels-Alderase" candidates. The four currently proposed mechanisms (including the Diels-Alder one) for this reaction in water (as a first-order approximation of the enzymatic reaction) are evaluated by an exhaustive quantum mechanical search for possible transition states (728 were found in total). We find that the line between the recently proposed bis-pericyclic [J. Am. Chem. Soc. 2016, 138 (11), 3631] and Diels-Alder routes is blurred, and favorable transition states of both types may coexist. Application of the Curtin-Hammett principle, however, reveals that the bis-pericyclic mechanism accounts for ∼83% of the reaction flow in water, while the classical Diels-Alder mechanism contributes only ∼17%. The current findings provide a route for modeling this reaction inside the SpnF active site and inferring the catalytic architecture of possible Diels-Alderases.

Lanthanide Fluorobenzoates as Bio-Probes: a Quest for the Optimal Ligand Fluorination Degree.

The thorough study of fluorinated benzoates of lanthanides (Eu, Tb, Nd, Er, Yb, Gd, La, Lu) is reported. Their composition in single crystal and powder state revealed two predominant structural motifs. An in-depth luminescence study has been performed on the reported fluorobenzoates, showing, that terbium and europium complexes in solid state possess high luminescence intensity with the quantum yield of up to 69 %. High solubility in most organic solvents, as well as in water, combined with the high luminescence intensity in water solution and non-toxicity allowed the testing of europium complexes as bioprobes in cellulo. Among all tested fluorobenzoates, europium 2-fluorobenzoate dihydrate combined the best luminescent properties, thermodynamic stability, aqueous solubility, and non-toxicity, and was shown to be a viable bio-marker.

An Icosidodecahedral Supramolecule Based on Pentaphosphaferrocene: From a Disordered Average Structure to Individual Isomers.

Pentaphosphaferrocenes [CpR Fe(η5 -P5 )] (1) and CuI halides are excellent building blocks for the formation of discrete supramolecules. Herein, we demonstrate the potential of Cu(CF3 SO3 ) for the construction of the novel 2D polymer [{Cp*Fe(µ4 ,η5:1:1:1 -P5 )}{Cu(CF3 SO3 )}]n (2) and the unprecedented nanosphere (CH2 Cl2 )1.4 @[{CpBn Fe(η5 -P5 )}12 {Cu(CF3 SO3 )}19.6 ] (3). The supramolecule 3 has a unique scaffold beyond the fullerene topology, with 20 copper atoms statistically distributed over the 30 vertices of an icosidodecahedron. Combinatorics was used to interpret the average disordered structure of the supramolecules. In this case, only two pairs of enantiomers with D5 and D2 symmetry are possible for bidentate bridging coordination of the triflate ligands. DFT calculations showed that differences in the energies of the isomers are negligible. The benzyl ligands enhance the solubility of 3, enabling NMR-spectroscopic and mass-spectrometric investigations.

Highly Luminescent, Water-Soluble Lanthanide Fluorobenzoates: Syntheses, Structures and Photophysics, Part I: Lanthanide Pentafluorobenzoates.

Highly luminescent, photostable, and soluble lanthanide pentafluorobenzoates have been synthesized and thoroughly characterized, with a focus on Eu(III) and Tb(III) complexes as visible emitters and Nd(III) , Er(III) , and Yb(III) complexes as infrared emitters. Investigation of the crystal structures of the complexes in powder form and as single crystals by using X-ray diffraction revealed five different structural types, including monomeric, dimeric, and polymeric. The local structure in different solutions was studied by using X-ray absorption spectroscopy. The photoluminescence quantum yields (PLQYs) of terbium and europium complexes were 39 and 15 %, respectively; the latter value was increased almost twice by using the heterometallic complex [Tb0.5 Eu0.5 (pfb)3 (H2 O)] (Hpfb=pentafluorobenzoic acid). Due to the effectively utilized sensitization strategy (pfb)(-) →Tb→Eu, a pure europium luminescence with a PLQY of 29 % was achieved.

Stabilization of 1T-MoS2 Sheets by Imidazolium Molecules in Self-Assembling Hetero-layered Nanocrystals.

We report a facile, room-temperature assembly of MoS2-based hetero-layered nanocrystals (NCs) containing embedded monolayers of imidazolium (Im), 1-butyl-3-methylimidazolium (BuMeIm), 2-phenylimidazolium, and 2-methylbenzimidazolium molecules. The NCs are readily formed in water solutions by self-organization of the negatively charged, chemically exfoliated 0.6 nm thick MoS2 sheets and corresponding cationic imidazole moieties. As evidenced by transmission electron microscopy, the obtained NCs are anisotropic in shape, with thickness varying in the range 5-20 nm and lateral dimensions of hundreds of nanometers. The NCs exhibit almost turbostratic stacking of the MoS2 sheets, though the local order is preserved in the orientation of the imidazolium molecules with respect to the sulfide sheets. The atomic structure of NCs with BuMeIm molecules was solved from powder X-ray diffraction data assisted by density functional theory calculations. The performed studies evidenced that the MoS2 sheets of the NCs are of the nonconventional 1T-MoS2 (metallically conducting) structure. The sheets' puckered outer surface is formed by the S atoms and the positioning of the BuMeIm molecules follows the sheet nanorelief. According to thermal analysis data, the presence of the BuMeIm cations significantly increases the stability of the 1T-MoS2 modification and raises the temperature for its transition to the conventional 2H-MoS2 (semiconductive) counterpart by ∼70 °C as compared to pure 1T-MoS2 (∼100 °C). The stabilizing interaction energy between inorganic and organic layers was estimated as 21.7 kcal/mol from the calculated electron density distribution. The results suggest a potential for the design of few-layer electronic devices exploiting the charge transport properties of monolayer thin MoS2.

Electronic structure of cesium butyratouranylate(VI) as derived from DFT-assisted powder X-ray diffraction data.

Investigation of chemical bonding and electronic structure of coordination polymers that do not form high-quality single crystals requires special techniques. Here, we report the molecular and electronic structure of the first cesium butyratouranylate, Cs[UO(2)(n-C(3)H(7)COO)(3)][UO(2)(n-C(3)H(7)COO)(OH)(H2O)], as obtained from DFT-assisted powder X-ray diffraction data because of the low quality of crystalline sample. The topological analysis of the charge distribution within the quantum theory of atoms-in-molecules (QTAIM) space partitioning and the distribution of electron localization function (ELF) is reported. The constancy of atomic domain of the uranium(VI) atom at different coordination numbers (7 and 8) and the presence of three ELF maxima in equatorial plane of an uranyl cation attributed to the 6s and 6p electrons were demonstrated for the first time. Details of methodologies applied for additional verification of the correctness of powder XRD refinement (Voronoi atomic descriptors and the Morse restraints) are discussed.

Crystal structure of ammonium 3'-azido-3'-de-oxy-thymidine-5'-amino-carbonyl-phospho-nate hemi-hydrate: an anti-HIV agent.

The asymmetric unit of the title compound, NH4 (+)·C11H14N6O7P(-)·0.5H2O, contains one 3'-azido-3'-de-oxy-thymidine-5'amino-carbonyl-phospho-nate (ACP-AZT) anion, half of an NH4 (+) cation lying on a twofold rotation axis and in another position, occupied with equal probabilities of 0.5, an NH4 (+) cation and a water mol-ecule. The amide group of the ACP-AZT anion is disordered (occupancy ratio 0.5:0.5), with one part forming an N-H⋯O (involving C=O⋯H4N(+)) hydrogen bond and the other an O-H⋯N (involving C-NH2⋯OH2) hydrogen bond with the components of the split NH4 (+)/H2O position. The pseudorotation parameters of ACP-AZT set it apart from previously studied AZT and thymidine. In the crystal, the various components are linked by N-H⋯O, O-H⋯O, N-H⋯N, C-H⋯O and C-H⋯N hydrogen bonds, forming a three-dimensional framework.

Comment on "Pushing the frontiers of density functionals by solving the fractional electron problem".

Kirkpatrick et al. (Reports, 9 December 2021, p. 1385) trained a neural network-based DFT functional, DM21, on fractional-charge (FC) and fractional-spin (FS) systems, and they claim that it has outstanding accuracy for chemical systems exhibiting strong correlation. Here, we show that the ability of DM21 to generalize the behavior of such systems does not follow from the published results and requires revisiting.

Stereoelectronic effects in N-C-S and N-N-C systems: experimental and ab initio AIM study.

The energy of stereoelectronic interactions in N-C-S and N-N-C systems in tetrahydro[1,3,4]thiadiazolo[3,4- c][1,3,4]thiadiazole was estimated by means of R. W. Bader's quantum theory of "atoms in molecules" (AIM) and natural bond orbital analysis (NBO). The results were compared with those obtained by analysis of rho( r) derived from high-resolution X-ray diffraction data. The analysis of the data obtained allowed one to find a correlation between geometric characteristics of the stereoelectronic interactions, NBO mixing energies and the AIM properties of atoms. Significant variations of nitrogen atom atomic basin populations in different conformers were explained by sterical interactions between their electron lone pairs.

The peculiarities of complex formation and energy transfer processes in lanthanide complexes with 2-(tosylamino)-benzylidene-N-benzoylhydrazone.

Depending on the local excess of lanthanide ions (Ln = Lu, Yb, Er, Dy, Tb, Gd, Eu, Nd) or 2-(tosylamino)-benzylidene-N-benzoylhydrazone (H2L), lanthanide complexes, containing either a mono-deprotonated ligand (Ln(HL)2X, X = Cl, NO3) or both mono- and dideprotonated ligands (Ln(L)(HL)), were preparatively obtained. The crystal structures of Lu(HL)2Cl, Yb(L)(HL)(H2O)2, Yb(L)(HL)(EtOH)2(H2O) and Er(L)(HL), determined by single crystal diffraction data or from powder diffraction data using Rietveld refinement, have shown the surprising resemblance. The study of luminescence temperature dependence of Eu(HL)2Cl and Eu(L)(HL) showed that europium luminescence is quenched by thermally-activated 5D0 → T1 energy transfer. Luminescent thermometers based on these complexes demonstrated the sensitivity of up to 7.7% at 85 K which is the highest value above liquid-nitrogen temperatures obtained to date.

New structure for the O-polysaccharide of Providencia alcalifaciens O27 and revised structure for the O-polysaccharide of Providencia stuartii O43.

The O-polysaccharide was obtained by mild acid degradation of the lipopolysaccharide from Providencia alcalifaciens O27 and studied by sugar and methylation analyses along with (1)H and (13)C NMR spectroscopy, including 2D (1)H,(1)H COSY, TOCSY, ROESY, H-detected (1)H,(13)C HSQC, and HMBC experiments. It was found that the polysaccharide is built up of linear partially O-acetylated tetrasaccharide repeating units and has the following structure: [structure: see text] where Qui4NFo stands for 4-formamido-4,6-dideoxyglucose (4-formamido-4-deoxyquinovose). The O-polysaccharide structure of Providencia stuartii O43 established earlier was revised with respect to the configuration of the constituent 4-amino-4,6-dideoxyhexose (from Rha4N to Qui4N).

Structure of the O-polysaccharide and serological cross-reactivity of the lipopolysaccharide of Providencia alcalifaciens O32 containing N-acetylisomuramic acid.

The O-polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of Providencia alcalifaciens O32 and studied by sugar and methylation analyses, solvolysis with triflic acid, 1H and 13C NMR spectroscopy, including two-dimensional 1H,1H COSY, TOCSY, ROESY, H-detected 1H,13C HSQC and HMBC experiments. It was found that the polysaccharide has a branched tetrasaccharide repeating unit containing 2-acetamido-3-O-[(S)-1-carboxyethyl]-2-deoxy-D-glucose (D-GlcNAc3Slac, N-acetylisomuramic acid) with the following structure: [ STRUCTURE: SEE TEXT]. Serological studies with O-antisera showed antigenic relationships between P. alcalifaciens O32 and O29 as well as several other Providencia and Proteus strains sharing putative epitopes on the O-polysaccharides.

Response to Comment on "Density functional theory is straying from the path toward the exact functional".

Kepp argues in his Comment, among other concerns, that the atomic densities we have considered are not relevant to molecular bonding. However, this does not change the main conclusion of our study, that unconstrained fitting of flexible functional forms can make a density functional more interpolative but less widely predictive.

Density functional theory is straying from the path toward the exact functional.

The theorems at the core of density functional theory (DFT) state that the energy of a many-electron system in its ground state is fully defined by its electron density distribution. This connection is made via the exact functional for the energy, which minimizes at the exact density. For years, DFT development focused on energies, implicitly assuming that functionals producing better energies become better approximations of the exact functional. We examined the other side of the coin: the energy-minimizing electron densities for atomic species, as produced by 128 historical and modern DFT functionals. We found that these densities became closer to the exact ones, reflecting theoretical advances, until the early 2000s, when this trend was reversed by unconstrained functionals sacrificing physical rigor for the flexibility of empirical fitting.

Structure of the O-polysaccharide from the lipopolysaccharide of Providencia alcalifaciens O29.

The O-polysaccharide was obtained by a mild acid degradation of the lipopolysaccharide of Providencia alcalifaciens O29. Structural studies were performed using sugar and methylation analyses along with 1H and 13C NMR spectroscopy, including two-dimensional 1H, 1H COSY, TOCSY, ROESY, H-detected 1H, 13C HSQC and HMBC experiments. On the basis of the data obtained, the following structure of the branched tetrasaccharide repeating unit of the O-polysaccharide was established: [structure: see text].

Z-effect reversal in carboxylic acid associates.

The carboxylic group is a common fragment in synthetic compounds and biomolecules. Its conformation is assumed to be dominantly cis due to so-called Z-effect. However, in this study, we show that the nature of the H-bond acceptor in RCOOHX directly affects the conformational preference of the resulting supermolecule. This result is evident from the statistical analysis of available crystallographic data and was quantified using accurate quantum chemical calculations. We propose the term "supramolecular stereoelectronic effect" for the observed conformational preference. The likely reason for this is the interaction of the O-HX hydrogen bond with the C[double bond, length as m-dash]O double bond in the trans conformation, which in case of anionic X is strong enough to reverse the Z-effect. Explicit consideration of trans COOHX stabilization can help crystal structure predictions and biomolecular simulations. In particular, this effect plays a key role in the transition between the T6 and R6 forms of human insulin.

Electrostatic Origin of Stabilization in MoS2-Organic Nanocrystals.

Negatively charged molybdenum disulfide layers form stable organic-inorganic layered nanocrystals when reacted with organic cations in solution. The reasons why this self-assembly process leads to a single-phase compound with a well-defined interlayer distance in given conditions are, however, poorly understood to date. Here, for the first time, we quantify the interactions determining the cation packing and stability of the MoS2-organic nanocrystals and find that the main contribution arises from Coulomb forces. The study was performed on the series of new layered compounds of MoS2 with naphthalene derivatives, forming several distinct phases depending on reaction conditions. Starting with structural models derived from powder X-ray diffraction data and TEM, we evaluate their cohesion energy by modeling layer separation with periodic PW-DFT-D calculations. The results provide a reliable approach for estimation of the stability of MoS2-based heterolayered compounds.

The structure of the O-polysaccharide from the lipopolysaccharide of Providencia stuartii O57 containing an amide of D-galacturonic acid with L-alanine.

The O-polysaccharide (O-antigen) was obtained by mild acid degradation of the lipopolysaccharide of Providencia stuartii O57:H29. Studies by sugar and methylation analyses along with (1)H and (13)C NMR spectroscopy, including two-dimensional (1)H,(1)H COSY, TOCSY, ROESY, H-detected (1)H,(13)C HSQC, and HMBC experiments, showed that the polysaccharide contains an amide of D-galacturonic acid with L-alanine and has the following pentasaccharide repeating unit: [formula: see text]

Structure of the O-polysaccharide of Providencia stuartii O49.

The O-specific polysaccharide chain (O-antigen) of the lipopolysaccharide (LPS) of Providencia stuartii O49 was studied using sugar and methylation analyses along with 1H and 13C NMR spectroscopy, including two-dimensional COSY, TOCSY, ROESY, H-detected 1H, 13C HSQC and HMBC experiments. The polysaccharide was found to have the trisaccharide repeating unit with the following structure: -->6)-beta-D-Galp(1-->3)-beta-D-GalpNAc(1-->4)-alpha-D-Galp(1-->

Synthesis of isomeric isothiazolo[4',3':4,5]- and isothiazolo[4',5':4,5]thieno[3,2-b]pyrano[2,3-d]pyridines by combination of domino reactions.

Isothiazolothienopyridines have been prepared by a domino reaction (the SN2 reaction → the Thorpe-Ziegler reaction → the Thorpe-Guareschi reaction type) from disodium 4-cyanoisothiazole-3,5-dithiolate. By changing the order of addition of the alkylation reagents in the reaction with disodium 4-cyanoisothiazole-3,5-dithiolate both possible isomers of the isothiazolothienopyridines are synthesized. These isomers were further used in three-component domino reaction (the Knoevenagel reaction → the Michael reaction → the hetero-Thorpe-Ziegler reaction type) to obtain wide range of isomeric isothiazolothienopyranopyridines.