4,6-Dichloro-5-Nitrobenzofuroxan: Different Polymorphisms and DFT Investigation of Its Reactivity with Nucleophiles

This research focuses on the X-ray structure of 4,6-dichloro-5-nitrobenzofuroxan 1 and of some of its amino derivatives (4a, 4e, 4g, and 4l) and on DFT calculations concerning the nucleophilic reactivity of 1. We have found that by changing the solvent used for crystallization, it is possible to obtain 4,6-dichloro-5-nitrobenzofuroxan (1) in different polymorphic structures. Moreover, the different torsional angles observed for the nitro group in 1 and in its amino derivatives (4a, 4e, 4g, and 4l) are strictly dependent on the steric hindrance of the substituent at C-4. DFT calculations on the course of the nucleophilic substitution confirm the role of the condensed furoxan ring in altering the aromaticity of the carbocyclic frame, while chlorine atoms strongly influence the dihedral angle and the rotational barrier of the nitro group. These results corroborate previous observations based on experimental kinetic data and give a deep picture of the reaction with amines, which proceeds via a “non-aromatic” nucleophilic substitution.

Group Contribution Revisited: The Enthalpy of Formation of Organic Compounds with “Chemical Accuracy” Part II

Group contribution (GC) methods to predict thermochemical properties are eminently important to process design. We present a group contribution parametrization for the heat of formation of organic molecules exhibiting chemical accuracy, maximum 1 kcal/mol (4.2 kJ/mol) difference between experiment and model values while minimizing the number of parameters avoiding overfitting and therewith avoiding reduced predictability. Compared to the contemporary literature, this was successfully achieved by employing available literature high-quality and consistent experimental data, optimizing parameters group by group, and introducing additional parameters when chemical understanding was obtained supporting these. A further important result is the observation that the applicability of the group contribution approach breaks down with increasing substitution levels, i.e., more heavily alkyl-substituted molecules, the reason being a serious influence of substitution on the conformation of the flexible part of the entire molecule within particular valence angles and torsional angles affected, which cannot be accounted for by additional GC parameters with fixed numerical values.

Convertible and Constrained Nucleotides: The 2’-Deoxyribose 5’-C-Functionalization Approach, a French Touch

Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5’-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson–Crick base-pairing. We show that 5’-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5’-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids.

Crystal structure of the sesquihydrate of dehydroepiandrosterone propan-2-ylidene hydrazone: Participation of the hydrazonyl nitrogen atoms as acceptors in the elaborate hydrogen bond scheme

The crystal structure of the sesquihydrate of dehydroepiandrosterone propan-2-ylidene hydrazone, [(7)2·(H2O)3], isolated from a solution of dehydroepiandrosterone propan-2-ylidene hydrazone, (7), in moist ethanol at room temperature, has been determined from data collected at 100 K. The sesquihydrate recrystallizes in the orthorhombic space group, P212121 with Z = 8. The asymmetric unit of [(7)2·(H2O)3] consists of two independent molecules of the steroid, Mol A and Mol B, and three moles of water. The six membered saturated rings, A and C, in both molecules have ideal or near ideal chair shapes, the unsaturated rings, B, have the expected half-chair shapes, while the five-membered rings, D, have envelope shapes with flaps at C114 and C214 for Mol A and Mol B, respectively. Differences in the conformations of the two molecules reside essentially completely within the hydrazonyl fragments with significantly different torsional angles, C117-N120-N121-C122 (in Mol A) and C217-N220-N221-C222 (in Mol B), of 149.19(14) and -93.08(17)°, respectively. The difference in this torsional angle is reflected in the hydrogen bonds involving the nitrogen atoms in the hydrazonyl units: it is of interest that the hydrazonyl nitrogen atoms partake as acceptors in hydrogen bonding with water molecules. The only intermolecular interactions in these molecules are hydrogen bonds -all classical O-H-O and OH···N hydrogen bonds with just one exception, a C-H···O(water) hydrogen bond. Of interest, there are no direct steroid-steroid links: molecules are linked solely by hydrogen bonds involving the hydrate molecules. All three hydrate molecules take part in the indirect linking of the steroid molecules, but each has its own set of contacts.

Computational approaches to amino acid side-chain conformation using combined NMR theoretical and experimental results: leucine-67 in Desulfovibrio vulgaris flavodoxin

In this paper, we show that the combination of NMR theoretical and experimental results can help to solve the molecular structure of peptides, here it is used as an example the residue Leucine-67 in Desulfovibrio vulgaris flavodoxin. We apply a computational protocol based on the leucine amino acid dipeptide, which, using calculated and experimental spin–spin coupling constants, allows us to obtain the conformation of the amino acid side chain. Calculated results show that the best agreement is obtained when three conformers around the lateral chain angle $\chi _1$ are considered or when the dynamic effect in the torsional angles is included. The population of each structure is estimated and analyzed according to the correlation between those two approaches. Independently of the approach, the estimated $\chi _1$ angle in solution is close to the staggered value of -60$^\circ $ and deviates significantly from the average x-ray angle of -90$^\circ $.

Auxiliary Atomic Relay Center Facilitates Enhanced Magnetic Couplings in Blatter’s Radical

<div>The recent accomplishments in obtaining the strong ferromagnetic exchange interactions in organic diradicals have made the field quite fascinating and even more promising towards its technological applications. In this context, herein we report a unique combination of remarkably strong ferromagnetic exchange interactions coupled with the molecular rigidity utilizing super-stable Blatter’s radical as a spin source. The planar analogues of the parent Blatter’s radical obtained by annulation with a chalcogen coupled to nitronyl nitroxide (NN) are investigated using density functional theory (DFT) along with the wave function based multi-configurational self-consistent field (MCSCF) methods e.g. CASSCF/NEVPT2. The calculations reveal phenomenal modulation in exchange couplings upon annulation such that remarkably strong ferromagnetic interactions are realized especially for a certain class of the Blatter - nitronyl nitroxide diradicals. The modulation of spin spin interactions is rationalised by variation in spin density distribution and molecular torsional angles. We demonstrate that annulation in OMMs opens an additional coupling pathway via auxiliary X-atom acting as atomic relay center which strongly manipulates the magnitude of exchange couplings.</div>

Auxiliary Atomic Relay Center Facilitates Enhanced Magnetic Couplings in Blatter’s Radical

<div>The recent accomplishments in obtaining the strong ferromagnetic exchange interactions in organic diradicals have made the field quite fascinating and even more promising towards its technological applications. In this context, herein we report a unique combination of remarkably strong ferromagnetic exchange interactions coupled with the molecular rigidity utilizing super-stable Blatter’s radical as a spin source. The planar analogues of the parent Blatter’s radical obtained by annulation with a chalcogen coupled to nitronyl nitroxide (NN) are investigated using density functional theory (DFT) along with the wave function based multi-configurational self-consistent field (MCSCF) methods e.g. CASSCF/NEVPT2. The calculations reveal phenomenal modulation in exchange couplings upon annulation such that remarkably strong ferromagnetic interactions are realized especially for a certain class of the Blatter - nitronyl nitroxide diradicals. The modulation of spin spin interactions is rationalised by variation in spin density distribution and molecular torsional angles. We demonstrate that annulation in OMMs opens an additional coupling pathway via auxiliary X-atom acting as atomic relay center which strongly manipulates the magnitude of exchange couplings.</div>

The Case for Methyl Group Precession Accompanying Torsional Motion

For molecules containing a methyl group, high precision fits of rotational line data (microwave spectra) that encompass several torsional states require considerably more constants than are required in comparable rigid molecules. Many of these additional terms are ‘torsion-rotation interaction’ terms, but their precise physical meaning is unclear. In this paper, we explore the physical origins of many of these additional terms in the case where the methyl group is attached to a planar frame. We show that torsion-vibration coupling, which has been observed in toluene and several substituted toluenes, provides the dominant contribution to a number of the torsion-rotation constants in toluene. It is further demonstrated that this coupling is intimately related to precession of the methyl group. A number of the constants required in the high resolution fits of rotational line data are shown to arise as a natural consequence of methyl precession. By considering several molecules whose rotational line spectra have been fit to high precision, we demonstrate that the experimental evidence is consistent with the occurrence of methyl group precession. Quantum chemistry calculations of the optimised molecular structures at key torsional angles provide further evidence that methyl precession occurs. There is both a torsional angle dependent tilt of the Cmethyl-frame bond and of the methyl group principal rotation axis relative to the Cmethyl-frame bond.

Combined XRD-paramagnetic 13C NMR spectroscopy of 1,2,3-triazoles for revealing copper traces in a Huisgen click-chemistry cycloaddition. A model case

Copper-catalyzed Alkyne-Azide Cycloaddition (CuAAC) click chemistry robustness has been demonstrated over recent years to produce 1,2,3-triazoles with excellent yields at mild conditions with simple purification methods. However, the consequences of having copper paramagnetic traces in final products, which complicate spectroscopic assignments and can produce inaccurate conclusions, has been scarcely discussed. Herein we present a strategy that combines X-Ray Diffraction (XRD) with 13C- paramagnetic Nuclear Magnetic Resonance spectroscopy, in order to demonstrate the presence of paramagnetic metal traces at standard Huisgen synthesis and purification conditions. We also demonstrate that the derivatization of 1,4-disubstituted-1,2,3-triazoles to produce 1,3,4,-trisubstituted-1,2,3.triazolium salts, promotes an efficient removal of Cu(II/I) moieties. Evidence of paramagnetic metal moieties is given using XRD structural analysis of abnormalities in torsional angles between substituents and the 1,2,3-triazole center, in parallel to 13C- paramagnetic NMR chemical shift and line width analysis. As model systems to demonstrate the importance of characterizing paramagnetic traces, we present the synthesis of novel 1-((3s,5s,7s)-adamantan-1-yl)-4-cyclopropyl-1H-1,2,3-triazole and its derivatized 1-((3s,5s,7s)-adamantan-1-yl)-4-cyclopropyl-3-methyl-1H-[1,2,3]-triazol-3-ium triflate salt.

Synthesis and Crystal Structure of Bis(2-phenylpyridine-C,N’)-bis(acetonitrile)iridium(III)hexafluorophosphate Showing Three Anion/Cation Couples in the Asymmetric Unit

The title compound bis(2-phenylpyridine-C,N’)-bis(acetonitrile)iridium(III)hexafluorophosphate, a six-coordinate iridium(III) complex, crystallizes in the P-1 space group. Iridium is in a distorted octahedral (n = 6) coordination with the N,C’ atoms of two phenylpyridine and the N atoms of two acetonitrile ligands. The peculiarity of this structure is that three independent moieties of the title compound and three PF6− anions, to counterbalance the charge, are observed in the asymmetric unit and this is a rather uncommon fact among the Cambridge Crystallographic Database (CSD) entries. The three couples are almost identical conformers with very similar torsional angles. The packing, symmetry, and space group were accurately analyzed and described also by means of Hirshfeld surface analysis, which is able to underline subtle differences among the three anion/cation couples in the asymmetric unit. The driving force of the packing is the clustering of the aromatic rings and the maximization of acetonitrile:PF6− interactions. The asymmetry of the cluster is the cause of the unusual number of moieties in the asymmetric unit.