Conformation In Solid State Research Articles

Synthesis and physicochemical evaluation of tetrafluorinated GABA analogue

Synthesis of 2,2,3,3-tetraftluoro-γ-aminobutyric acid (tetraF-GABA) starting from commercially available 2,2,3,3-tetrafluorobutane-1,4-diol is described. The straightforward nine-step reaction sequence allowed the production of up to 20 g of the target amino acid in 41 % overall yield. Potentiometric titration revealed increased acidity of both ionizable moieties in the title compound (the pKa values were diminished by 1.6 and 4.0 units for the COOH and NH3+ groups, respectively, as compared to parent GABA). X-ray diffraction studies and DFT calculations demonstrated different preferential conformations in solid state and solution, although the fluorine gauche effect was observed in both cases.

Recent progress on solid-state cross-polarization (CP)/magic angle spinning (MAS) NMR measurements: a tool for investigating structural changes in stimuli-responsive organic compounds

Abstract Over the years, cross-polarization/magic angle sample spinning (CP/MAS) NMR has proven to be valuable for obtaining detailed structural information in solid-state materials. A notable advantage of this technique is that it does not require a well-organized arrangement in the sample such as single crystals. Consequently, even materials with low crystallinity such as amorphous substances can be analyzed to obtain structural information. In recent years, research on externally stimuli-responsive molecules utilizing crystal phase transitions has attracted attention. Certain aryl disilane and oligosilane compounds exhibit external stimulus responsiveness even in the crystalline state due to the hindered rotation of the Si–Si σ bond and sparse crystal packing. Understanding the structural alternations linked to changes in physical properties is crucial for investigation of the responsiveness. High-resolution CP/MAS NMR spectra are particularly suitable for analyzing crystalline polymorphs, crystal phase transitions, and solid-state conformations. In this report, we present the results of natural abundance 13C, 29Si, and 15N CP/MAS NMR experiments conducted on externally stimuli-responsive disilane-bridged molecules. These measurements provide information on the structure before and after crystal phase transitions, as well as the amorphous state. A comprehensive analysis of our findings is essential for elucidating alternations in the structure and arrangement of crystalline materials under external stimuli.

Desolvation Induced Conformational Transition in a Cryptophane Host: Crystal To Crystal Transformation.

Cryptophanes show different conformations in solution and solid state depending upon various factors, such as the length of connecting linkers, medium, and nature of the incoming guest molecule(s). A cyclotriguaiacylenes (CTG) based cryptophane molecule was synthesized using click chemistry containing three triazole linkers and studied as well. This molecule shows two conformations, out-out crown-crown (CC), and out-in CC, in the presence or absence of guest molecule(s), as studied both in solution and solid state. The out-in CC, in which both CTG fragments are in crown conformation with one crown sitting above the other, could be obtained by slow escape of the trapped acetone molecules from out-out CC in solid state. This transformation could be obtained through a single-crystal-to-single-crystal (SCSC) transformation from a large volume out-out CC to a smaller volume out-in CC conformation which is also supported by density functional theory calculations.

Short I⋯O Interactions in the Crystal Structures of Two 2-Iodo-Phenyl Methyl-Amides as Substrates for Radical Translocation Reactions

Radical translocation reactions are finding various uses in organic synthesis, in particular the stereospecific formation of complex natural products. In this work, the syntheses and single-crystal structures of two substituted 2-iodo-phenyl methyl-amides are reported, namely cyclo-propane carboxylic acid (2-iodo-phenyl)-methyl-amide, C11H12INO (1), and cyclo-heptane carboxylic acid (2-iodo-phenyl)-methyl-amide, C15H20INO (2). In each case, the methyl-amide group has a syn conformation, and this grouping is perpendicular to the plane of the benzene ring: these solid-state conformations appear to be well setup to allow an intramolecular hydrogen atom transfer to take place as part of a radical translocation reaction. Short intermolecular I⋯O halogen bonds occur in each crystal structure, leading to [010] chains in 1 [I⋯O = 3.012 (2) Å] and isolated dimers in 2 [I⋯O = 3.024 (4) and 3.057 (4) Å]. The intermolecular interactions are further quantified by Hirshfeld surface analyses.

Conformational flexibility of the disaccharide β-L-Fucp-(1→4)-α-D-Glcp-OMe as deduced from NMR spectroscopy experiments and computer simulations.

Carbohydrates in biological systems are referred to as glycans and modification of their structures is a hallmark indicator of disease. Analysis of the three-dimensional structure forms the basis for further insight into how they function and comparison of crystal structure with solution-state conformation(s) is particularly relevant, which has been performed for the disaccharide β-L-Fucp-(1→4)-α-D-Glcp-OMe. In water solution the conformational space at the glycosidic linkage between the two sugar residues is identified from molecular dynamics (MD) simulations as having a low-energy exo-syn conformation, deviating somewhat from the solid-state conformation, and two anti-conformational states, i.e., anti-ϕ and anti-ψ, indicating flexibility at the glycosidic linkage. NMR data were obtained from 1D 1H,1H-NOESY and STEP-NOESY experiments, measurement of transglycosidic 3JCH coupling constants and NMR spin-simulation. The free energy profile of the ω torsion angle computed from MD simulation was in excellent agreement with the rotamer distribution from NMR experiment being for gt:gg:tg 38 : 53 : 9, respectively, with a proposed inter-residue O5'⋯HO6 hydrogen bond being predominant in the gg rotamer. Quantum mechanics methodology was used to calculate transglycosidic NMR 3JCH coupling constants, averaged over a conformational ensemble of structures representing various rotamers of exocyclic groups, in good to excellent agreement with Karplus-type relationships previously developed. Furthermore, 1H and 13C NMR chemical shifts were calculated using the same methodology and were found to be in excellent agreement with experimental data.

Structure and Conformation of Novel BODIPY Ugi Adducts.

Two novel BODIPY‐Ugi (boron dipyrromethene) adducts exhibit peculiar room temperature (T=20 °C) H‐1 NMR spectra in that several protons located at the aromatic aniline‐type ring are lost in the baseline. This observation revealed the existence of a dynamic conformational process where rotation around the C−N bond is hindered. Variable‐temperature H‐1 and C‐13 NMR spectroscopic analysis confirmed this conclusion; that is, low‐temperature spectra show distinct signals for all four aromatic protons below coalescence, whereas average signals are recorded above coalescence (T=+120 °C). Particularly interesting was the rather large difference in chemical shifts for the ortho protons below coalescence, Δδ=1.45 ppm, which was explained based on DFT computational analysis. Indeed, the calculated lowest‐energy gas‐phase conformation of the BODIPY Ugi adducts locates one half of the aniline‐type ring in the shielding anisotropic cone of the bridge phenyl ring in the BODIPY segment. This is in contrast to the solid‐state conformation established by X‐ray diffraction analysis that shows a nearly parallel arrangement of the aromatic rings, probably induced by crystal packing forces.

Ornamenting of Blue Thermally Activated Delayed Fluorescence Emitters by Anchor Groups for the Minimization of Solid-State Solvation and Conformation Disorder Corollaries in Non-Doped and Doped Organic Light-Emitting Diodes.

Motivated to minimize the effects of solid-state solvation and conformation disorder on emission properties of donor–acceptor-type emitters, we developed five new asymmetric multiple donor–acceptor type derivatives of tert-butyl carbazole and trifluoromethyl benzene exploiting different electron-accepting anchoring groups. Using this design strategy, for a compound containing four di-tert-butyl carbazole units as donors as well as 5-methyl pyrimidine and trifluoromethyl acceptor moieties, small singlet-triplet splitting of ca. 0.03 eV, reverse intersystem crossing rate of 1 × 106 s–1, and high photoluminescence quantum yield of neat film of ca. 75% were achieved. This compound was also characterized by the high value of hole and electron mobilities of 8.9 × 10–4 and 5.8 × 10–4 cm2 V–1 s–1 at an electric field of 4.7 × 105 V/cm, showing relatively good hole/electron balance, respectively. Due to the lowest conformational disorder and solid-state solvation effects, this compound demonstrated very similar emission properties (emission colors) in non-doped and differently doped organic light-emitting diodes (OLEDs). The lowest conformational disorder was observed for the compound with the additional accepting moiety inducing steric hindrance, limiting donor–acceptor dihedral rotational freedom. It can be exploited in the multi-donor–acceptor approach, increasing the efficiency. Using an emitter exhibiting the minimized solid-state solvation and conformation disorder effects, the sky blue OLED with the emitting layer of this compound dispersed in host 1,3-bis(N-carbazolyl)benzene displayed an emission peak at 477 nm, high brightness over 39 000 cd/m2, and external quantum efficiency up to 15.9% along with a maximum current efficiency of 42.6 cd/A and a maximum power efficiency of 24.1 lm/W.

Crystal structure of merimepodib, C23H24N4O6

The crystal structure of merimepodib has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Merimepodib crystallizes in space group P212121 (#19) with a = 4.60827(3), b = 12.30400(14), c = 37.9583(4) Å, V = 2152.241(20) Å3, and Z = 4. The crystal structure is dominated by two chains of N–H⋯O hydrogen bonds along the a-axis. The solid-state conformation has a similar general shape to the minimum-energy conformation, but different orientations of several of the rings. The differences indicate that intermolecular interactions are important in determining the solid-state conformation. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

"Rim-Differentiated" Pillar[6]arenes.

A "rim-differentiated" pillar[6]arene (RD-P[6]) was obtained successfully, with the assistance of a dimeric silver trifluoroacetate template, among eight different constitutional isomers in a direct and regioselective manner. The solid-state conformation of this macrocycle could switch from the 1,3,5-alternate to a truly rim-differentiated one upon guest inclusion. This highly symmetric RD-P[6] not only hosts metal-containing molecules inside its cavity, but also can form a pillar[6]arene-C60 adduct through co-crystallization on account of donor-acceptor interactions. The development of synthetic strategies to desymmetrize pillararenes offers new opportunities for engineering complex molecular architectures and organic electronic materials.

Triglycine (GGG) Adopts a Polyproline II (pPII) Conformation in Its Hydrated Crystal Form: Revealing the Role of Water in Peptide Crystallization.

Polyproline II (pPII) is a left-handed 31-helix conformation, which has been observed to be the most abundant secondary structure in unfolded peptides and proteins compared to α-helix and β-sheet. Although pPII has been reported as the most stable conformation for several unfolded short chain peptides in aqueous solution, it is rarely observed in their solid state. Here, we show for the first time a glycine homopeptide (gly-gly-gly) adopting the pPII conformation in its crystalline dihydrate structure. The single crystal X-ray structure with molecular dynamic simulation suggests that a network of water and the charged carboxylate group is critical in stabilizing the pPII conformation in solid state, offering an insight into the structures of unfolded regions of proteins and the role of water in peptide crystallization.

Effect of the nO → π*C═O Interaction on the Conformational Preference of 1,3-Diketones: A Case Study of Riolozatrione Derivatives.

The cyclopropane ring-opening reaction of riolozatrione, a natural product obtained from Jatropha dioica, afforded a 2,2-disubstituted 1,3-cyclohexandione displaying an alkyl methyl ether group at position 5. The conformational analysis of this product showed a high preference for the trans-diaxial conformation in both solution and solid state. Such conformation was possible from the noncovalent intramolecular nX → π*C═O interactions (X = an element having an unshared electron pair), allowing the determination of the interaction energies. Since the nX → π*C═O interactions can be regarded as additive, the energy values ranged from 4.52 to 6.51 kcal mol-1 for each carbonyl group with a strong dependency on the interatomic distances. The rigorous analysis of the electron density in the topological theory of atoms in molecules framework clearly shows that the origin of O-C═O interactions are through the nO → π*C═O electron transfer mechanism. Such interactions are slightly weaker than a canonical hydrogen bond but seemingly stronger than a van der Waals interaction. This interaction must be considered as a stereoelectronic effect due the electronic transfer between the interacting groups, which are limited by their relative stereochemistry and can be represented by a bond-no bond interaction, causing the pyramidalization of the carbonyl, which is the charge acceptor group.

Still Relevant Today: The Asinger Multicomponent Reaction.

The Asinger multicomponent reaction is a versatile synthetic tool which gives access to multiple drug-like scaffolds such as 3-thiazolines. The diversity and easy access of its starting materials, its operational simplicity combined with mild conditions and relatively good yields, renders the Asinger reaction, today more than ever, a cornerstone not only in heterocyclic chemistry and modern synthesis but also in medicinal chemistry. In this review, we perform a thorough analysis of the scope and limitations on the different reaction variants with their starting materials, the three-dimensional solid-state conformations of the Asinger derivatives, and we underline and classify all the major post-modifications that have been described. In addition, we report all the major applications in drug discovery projects.

Thiazole\u2013amino acids: influence of thiazole ring on conformational properties of amino acid residues

Post-translational modified thiazole–amino acid (Xaa–Tzl) residues have been found in macrocyclic peptides (e.g., thiopeptides and cyanobactins), which mostly inhibit protein synthesis in Gram + bacteria. Conformational study of the series of model compounds containing this structural motif with alanine, dehydroalanine, dehydrobutyrine and dehydrophenylalanine were performed using DFT method in various environments. The solid-state crystal structure conformations of thiazole–amino acid residues retrieved from the Cambridge Structural Database were also analysed. The studied structural units tend to adopt the unique semi-extended β2 conformation; which is stabilised mainly by N–H⋯NTzl hydrogen bond, and for dehydroamino acids also by π-electron conjugation. The conformational preferences of amino acids with a thiazole ring were compared with oxazole analogues and the role of the sulfur atom in stabilising the conformations of studied peptides was discussed.

Targeting KRAS Mutant Cancers via Combination Treatment: Discovery of a 5-Fluoro-4-(3H)-quinazolinone Aryl Urea pan-RAF Kinase Inhibitor.

Optimization of a series of aryl urea RAF inhibitors led to the identification of type II pan-RAF inhibitor GNE-0749 (7), which features a fluoroquinazolinone hinge-binding motif. By minimizing reliance on common polar hinge contacts, this hinge binder allows for a greater contribution of RAF-specific residue interactions, resulting in exquisite kinase selectivity. Strategic substitution of fluorine at the C5 position efficiently masked the adjacent polar NH functionality and increased solubility by impeding a solid-state conformation associated with stronger crystal packing of the molecule. The resulting improvements in permeability and solubility enabled oral dosing of 7. In vivo evaluation of 7 in combination with the MEK inhibitor cobimetinib demonstrated synergistic pathway inhibition and significant tumor growth inhibition in a KRAS mutant xenograft mouse model.

Crystal structure of edoxaban tosylate monohydrate Form I, (C24H31ClN7O4S)(C7H7O3S)(H2O)

The crystal structure of edoxaban tosylate monohydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Edoxaban tosylate monohydrate crystallizes in space group P21 (#4) with a = 7.55097(2), b = 7.09010(2), c = 32.80420(21) Å, β = 96.6720(3)°, V = 1744.348(6) Å3, and Z = 2. The crystal structure consists of alternating layers of edoxaban cations and tosylate anions along the c-axis. The water molecules lie near the sulfonate end of the tosylate anions. The solid-state conformation of the edoxaban cation is determined by intermolecular interactions. The protonated nitrogen atom forms a strong N–H⋯O hydrogen bond to one of the tosylate oxygens. Only one of the water molecule hydrogens acts as a donor in an O–H⋯O hydrogen bond. The tosylate oxygens act as acceptors in a number of C–H⋯O hydrogen bonds. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

Crystal structure of pimecrolimus Form B, C43H68ClNO11

The crystal structure of pimecrolimus Form B has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Pimecrolimus crystallizes in the space group P21 (#4) with a = 15.28864(7), b = 13.31111(4), c = 10.95529(5) Å, β = 96.1542(3)°, V = 2216.649(9) Å3, and Z = 2. Although there are an intramolecular six-ring hydrogen bond and some larger chain and ring patterns, the crystal structure is dominated by van der Waals interactions. There is a significant difference between the conformation of the Rietveld-refined and the DFT-optimized structures in one portion of the macrocyclic ring. Although weak, intermolecular interactions are apparently important in determining the solid-state conformation. The powder pattern is included in the Powder Diffraction File™ (PDF®) as entry 00-066-1619. This study provides the atomic coordinates to be added to the PDF entry.

Crystal structure of (E)-doxepin hydrochloride, C19H22NOCl

The crystal structure of (E)-doxepin hydrochloride has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. (E)-doxepin hydrochloride crystallizes in space group P21/a (#14) with a = 13.78488(7), b = 8.96141(7), c = 14.30886(9) Å, β = 96.5409(5)°, V = 1756.097(12) Å3, and Z = 4. There is a strong discrete hydrogen bond between the protonated nitrogen atom and the chloride anion. There are six C–H⋯Cl hydrogen bonds between the methyl groups and the chloride, as well as additional hydrogen bonds from methylene groups and the vinyl proton. The hydrogen bonds are important in determining the solid-state conformation of the cation. The compound is essentially isostructural to amitriptyline hydrochloride. The powder pattern is included in the Powder Diffraction File™ as entry 00-066-1613.

From Carbohydrates to Complex Organofluorines: Synthesis, Conformation, and Lipophilicity of Multivicinal-Fluorine-Containing Hexitol Analogues.

There is growing interest in the preparation of fluorine-containing organic molecules. Multivicinal-fluorine analogues are among the most intriguing and promising compounds, but their physical and biological investigations are held back by challenging syntheses. Herein, we report on the synthesis of a large set of novel polyfluorohexitols. The dominant solution-state conformation of all trifluorohexitols was determined, and the solid-state conformations of some analogues were compared. Finally, the lipophilicity of a large set of polyfluorinated hexopyranose and hexitol analogues was attributed by using a log P determination method based on 19 F NMR spectroscopy.

Molecular dynamics study of structural properties of γ-aminobutyric acid (GABA)

The study of structural conformation of Gamma-aminobutyric acid (GABA) exhibits its biological and chemical activities. The GABA molecule is responsible in neurotransmission from one neuron to another neuron and activates the ion channels to pass the chlorine and sodium ions in nerve cells. Its conformation in solid state and gas state are extremely different and it also shows five different conformations in aqueous solution. The study of its structure in such environment can reveal its activity in cellular environment. We have performed the classical molecular dynamics study of this system of GABA in aqueous medium to deal its structure. Radial distribution function (RDF) has been used to study the structural properties of the system.
 BIBECHANA 18 (2021) 67-74

Minimization of Solid-State Solvation and Conformation Disorder Corollaries on Performance of Blue TADF Emitters by Multi-Donor-Acceptor Substitution Engineering

Minimization of Solid-State Solvation and Conformation Disorder Corollaries on Performance of Blue TADF Emitters by Multi-Donor-Acceptor Substitution Engineering