Energetic Aspects and Molecular Mechanism of 3-Nitro-substituted 2-Isoxazolines Formation via Nitrile N-Oxide [3+2] Cycloaddition: An MEDT Computational Study.

Regioselectivity and the molecular mechanism of the [3+2] cycloaddition reaction between nitro-substituted formonitrile N-oxide 1 and electron-rich alkenes were explored on the basis of the wb97xd/6-311+G(d) (PCM) quantum chemical calculations. It was established that the thermodynamic factors allow for the formation of stable cycloadducts along all considered models. The analysis of the kinetic parameters of the main processes show that all [3+2] cycloadditions should be realized with full regioselectivity. In all cases, the formation of 5-substituted 3-nitro-2-isoxazolidines is clearly preferred. It is interesting that regiodirection is not determined by the local electrophile/nucleophile interactions but by steric effects. From a mechanistic point of view, all considered reactions should be treated as polar, one-step reactions. All attempts to locate the hypothetical zwitterionic intermediates along the cycloaddition paths were, however, not successful.

Influence of heterochirality on the structure, dynamics, biological properties of cyclic(PFPF) tetrapeptides obtained by solvent-free ball mill mechanosynthesis.

Cyclic tetrapeptides c(Pro-Phe-Pro-Phe) obtained by the mechanosynthetic method using a ball mill were isolated in a pure stereochemical form as a homochiral system (all L-amino acids, sample A) and as a heterochiral system with D configuration at one of the stereogenic centers of Phe (sample B). The structure and stereochemistry of both samples were determined by X-ray diffraction studies of single crystals. In DMSO and acetonitrile, sample A exists as an equimolar mixture of two conformers, while only one is monitored for sample B. The conformational space and energetic preferences for possible conformers were calculated using DFT methods. The distinctly different conformational flexibility of the two samples was experimentally proven by Variable Temperature (VT) and 2D EXSY NMR measurements. Both samples were docked to histone deacetylase HDAC8. Cytotoxic studies proved that none of the tested cyclic peptide is toxic.

Solvent-Free Mechanosynthesis of Oligopeptides by Coupling Peptide Segments of Different Lengths - Elucidating the Role of Cesium Carbonate in Ball Mill Processes.

We report an idea for the synthesis of oligopeptides using a solvent-free ball milling approach. Our concept is inspired by block play, in which it is possible to construct different objects using segments (blocks) of different sizes and lengths. We prove that by having a library of short peptides and employing the ball mill mechanosynthesis (BMMS) method, peptides can be easily coupled to form different oligopeptides with the desired functional and biological properties. Optimizing the BMMS process we found that the best yields we obtained when TBTU and cesium carbonate were used as reagents. The role of Cs2CO3 in the coupling mechanism was followed on each stage of synthesis by 1H, 13C and 133Cs NMR employing Magic Angle Spinning (MAS) techniques. It was found that cesium carbonate acts not only as a base but is also responsible for the activation of substrates and intermediates. The unique information about the BMMS mechanism is based on the analysis of 2D NMR data. The power of BMMS is proved by the example of different peptide combinations, 2+2, 3+2, 4+2, 5+2 and 4+4. The tetra-, penta-, hexa-, hepta- and octapeptides obtained under this project were fully characterized by MS and NMR techniques.

On the Question of Zwitterionic Intermediates in the [3+2] Cycloaddition Reactions between Aryl Azides and Ethyl Propiolate.

The molecular mechanism of the [3+2] cycloaddition reactions between aryl azides and ethyl propiolate was evaluated in the framework of the Molecular Electron Density Theory. It was found that independently of the nature of the substituent within the azide molecule, the cycloaddition process is realized via a polar but single-step mechanism. All attempts of localization as postulated earlier by Abu-Orabi and coworkers' zwitterionic intermediates were not successful. At the same time, the formation of zwitterions with an "extended" conformation is possible on parallel reaction paths. The ELF analysis shows that the studied cycloaddition reaction leading to the 1,4-triazole proceeds by a two-stage one-step mechanism. It also revealed that both zwitterions are created by the donation of the nitrogen atom's nonbonding electron densities to carbon atoms of ethyl propiolate.

Understanding the Molecular Mechanism of Thermal and LA-Catalysed Diels-Alder Reactions between Cyclopentadiene and Isopropyl 3-Nitroprop-2-Enate.

The molecular mechanism of the Diels-Alder reaction with the participation of cyclopentadiene and isopropyl 3-nitroprop-2-enate was examined based on wb97xd/6-311+G(d) (PCM) quantum chemical calculations. It was found that the type of mechanism for the conversion of addends depends significantly on the reaction conditions. In less-polar environments, a one-step polar mechanism is realised. In more polar solvents, the formation of "extended"-type zwitterionic intermediates is possible. In contrast, in the presence of an LA-type catalyst, the one-step mechanisms are replaced by respective stepwise mechanisms with zwitterionic or heterocyclic intermediates.

Fully Selective Synthesis of Spirocyclic-1,2-oxazine N-Oxides via Non-Catalysed Hetero Diels-Alder Reactions with the Participation of Cyanofunctionalysed Conjugated Nitroalkenes.

Hetero Diels-Alder (HDA) reactions with the participation of E-2-aryl-1-cyano-1-nitroethenes and methylenecyclopentane were evaluated on the basis of experimental as well as quantumchemical data. It was found that contrary to most known HDA reactions, title processes are realised under non-catalytic conditions and with full regiocontrol. The DFT study shows, without any doubt, the polar but single-step reaction mechanism. Deeper exploration using Bonding Evolution Theory (BET) techniques gives a clear image of the sequences of electron density reorganisation along the reaction coordinate. The first C4-C5 bond is created in phase VII by merging two monosynaptic basins, while the second O1-C6 bond is created in the last phase by a donation of the nonbonding electron density of O1 to C6. Based on the research, we can conclude that the analysed reaction proceeds according to a two-stage one-step mechanism.

On the Question of the Formation of Nitro-Functionalized 2,4-Pyrazole Analogs on the Basis of Nitrylimine Molecular Systems and 3,3,3-Trichloro-1-Nitroprop-1-Ene.

Experimental and theoretical studies on the reaction between (E)-3,3,3-trichloro-1-nitroprop-1-ene and N-(4-bromophenyl)-C-arylnitrylimine were performed. It was found that the title process unexpectedly led to 1-(4-bromophenyl)-3-phenyl-5-nitropyrazole instead of the expected Δ2-pyrazoline molecular system. This was the result of a unique CHCl3 elimination process. The observed mechanism of transformation was explained in the framework of the molecular electron density theory (MEDT). The theoretical results showed that both of the possible channels of [3 + 2] cycloaddition were favorable from a kinetic point of view, due to which the creation of 1-(4-bromophenyl)-3-aryl-4-tricholomethyl-5-nitro-Δ2-pyrazoline was more probable. On the other hand, according to the experimental data, the presented reactions occurred with full regioselectivity.

Understanding the Regioselectivity and the Molecular Mechanism of [3 + 2] Cycloaddition Reactions between Nitrous Oxide and Conjugated Nitroalkenes: A DFT Computational Study.

Regiochemical aspects and the molecular mechanism of the [3 + 2] cycloaddition between nitrous oxide and conjugated nitroalkenes were evaluated on the basis of the wb97xd/6-311 + G(d) (PCM) computational study. It was found that, independently of the nature of the nitroalkene, all considered processes are realized via polar, single-step mechanisms. All attempts at the localization of hypothetical zwitterionic intermediates were unsuccessful. Additionally, the DFT computational study suggested that, in the course of the reaction, the formation of respective Δ2-4-nitro-4-R1-5-R2-1-oxa-2,3-diazolines was preferred from the kinetic point of view.

The First Examples of [3+2] Cycloadditions with the Participation of (E)-3,3,3-Tribromo-1-Nitroprop-1-Ene.

The first examples of [3+2] cycloaddition reactions between 3,3,3-tribromo-1-nitroprop-1-ene (TBMN) were explored on the basis of experimental and theoretical approaches. It was found that reactions involving TBMN and diarylnitrones realized with full regio- and stereoselectivity lead to respective 3,4-cis-4,5-trans-4-nitroisoxazolidines. The regioselecticity and the molecular mechanism of title processes was analyzed on the basis of the advanced DFT computational study.

Structural variety of heterosynthons in linezolid cocrystals with modified thermal properties.

In a search for new crystalline forms of linezolid with modified thermal properties five cocrystals of this wide range antibiotic with aromatic acids were obtained via mechanochemical grinding and analyzed with single crystal X-ray diffraction, solid-state NMR spectroscopy, powder X-ray diffraction and DSC measurements. The coformers used in this study were benzoic acid, p-hydroxybenzoic acid, protocatechuic acid, γ-resorcylic acid and gallic acid. In each of the cocrystals distinct structural features have been found, including a variable amount of water and different heterosynthons, indicating that there is more than one type of intermolecular interaction preferred by the linezolid molecule. Basing on the frequency of the observed supramolecular synthons, the proposed hierarchy of the hydrogen-bond acceptor sites of linezolid (LIN) is C=Oamide > C=Ooxazolidone > C-O-Cmorpholine > C-N-Cmorpholine > C-O-Coxazolidone. In addition, aromatic-aromatic interactions were found to be important in the stabilization of the analyzed structures. The obtained cocrystals show modified thermal properties, with four of them having melting points lower than the temperature of the phase transition from linezolid form II to linezolid form III. Such a change in this physicochemical property allows for the future application of melting-based techniques of introducing linezolid into drug delivery systems. In addition a change in water solubility of linezolid upon cocrystalization was evaluated, but only in the case of the cocrystal with protocatechuic acid was there a significant (43%) improvement in solubility in comparison with linezolid.

Cocrystals "Divorce and Marriage": When a Binary System Meets an Active Multifunctional Synthon in a Ball Mill.

A well-defined and stable "AB" binary system in the presence of "C" a crystalline synthon ground in a ball mill undergoes selective transformation in the solid state according to the equation AB+C→AC+B. When the amount of C is increased two times then the equation AB+2C→AC+BC is valid. The other variants are more complex. The pathway BC+A is allowed and leads to the AC and B products. The pathway AC+B is not preferred, and no transformation is observed. These non-obvious correlations were observed for cocrystal of barbituric acid (BA):thiobarbituric acid (TBA) recently reported by Shemchuk et al. (Chem. Commun. 2016, 52, 11815-11818) in the presence of 1-hydroxy-4,5-dimethyl-imidazole 3-oxide (HIMO). This synthon shows high affinity for the BA0.5 TBA0.5 cocrystal as well for its individual components, BA and TBA. Single-quantum, double-quantum (SQ-DQ) 2D 1 H very fast MAS NMR with a spinning rate of 60 kHz was employed as a basic and most diagnostic tool for the study of cocrystals transformations. Analysis of the experimental data was supported by theoretical calculations, including computation of the stabilization energy, Estab , defined as the energy difference between the energy of a co-crystal and the sum of the energies of particular components in the respective stoichiometric ratios. Two mechanisms of synthon replacement have been proposed. Pathway 1 assumes a concerted mechanism of substitution. In this approach, synthon attack is synchronized in time with the departure of one of the components of the binary system. Pathway 2 implies a non-concerted process, with an intermediate stage in which three separate components are present. Evidence suggesting a preference for Pathway 2 is shown.

Application of 1-Hydroxy-4,5-Dimethyl-Imidazole 3-Oxide as Coformer in Formation of Pharmaceutical Cocrystals.

Two, well defined binary crystals with 1-Hydroxy-4,5-Dimethyl-Imidazole 3-Oxide (HIMO) as coformer and thiobarbituric acid (TBA) as well barbituric acid (BA) as Active Pharmaceutical Ingredients (APIs) were obtained by cocrystallization (from methanol) or mechanochemically by grinding. The progress of cocrystal formation in a ball mill was monitored by means of high-resolution, solid state NMR spectroscopy. The 13C CP/MAS, 15N CP/MAS and 1H Very Fast (VF) MAS NMR procedures were employed to inspect the tautomeric forms of the APIs, structure elucidation of the coformer and the obtained cocrystals. Single crystal X-ray studies allowed us to define the molecular structure and crystal packing for the coformer as well as the TBA/HIMO and BA/HIMO cocrystals. The intermolecular hydrogen bonding, π-π interactions and CH-π contacts responsible for higher order organization of supramolecular structures were determined. Biological studies of HIMO and the obtained cocrystals suggest that these complexes are not cytotoxic and can potentially be considered as therapeutic materials.

Porous Molecular Capsules as Non-Polymeric Transducers of Mechanical Forces to Mechanophores.

Mechanical grinding/milling can be regarded as historically the first technology for changing the properties of matter. Mechanically activated molecular units (mechanophores) can be present in various structures: polymers, macromolecules, or small molecules. However, only polymers have been reported to effectively transduce energy to mechanophores, which induces breakage of covalent bonds. In this paper, a second possibility is presented-molecular capsules as stress-sensitive units. Mechanochemical encapsulation of fullerenes in cystine-based covalent capsules indicates that complexation takes place in the solid state, despite the fact that the capsules do not possess large enough entrance portals. By using a set of solvent-free MALDI (sf-MALDI) and solid-state NMR (ss-NMR) experiments, it has been proven that encapsulation proceeds during milling and in this process hydrazones and disulfides get activated for breakage, exchange, and re-forming. The capsules are porous and therefore prone to collapse under solvent-free conditions and their conformational rigidity promotes the collapse by the breaking of covalent bonds.

Approach toward the Understanding of Coupling Mechanism for EDC Reagent in Solvent-Free Mechanosynthesis.

A unique approach in mechanosynthesis, joining solid-state NMR spectroscopy, X-ray crystallography, and theoretical calculations, is employed for the first time to study the mechanism of the formation of the C-N amide bond using EDC·HCl as a coupling reagent. It has been proved that EDC·HCl, which in the crystal lattice exists exclusively in the cyclic form (X-ray data), easily undergoes transformation to a pseudocyclic stable intermediate in reaction with carboxylic acid forming a low-melt phase (differential scanning calorimetry, solid-state NMR). The obtained intermediate is reactive and can be further used for synthesis of amides in reaction with appropriate amines.