Rotational Barriers Research Articles

Catalytic Asymmetric Synthesis of Atropisomers Featuring an Aza Axis.

ConspectusAtropisomers bearing a rotation-restricted axis are common structural units in natural products, chiral ligands, and drugs; thus, the prevalence of asymmetric synthesis has increased in recent decades. Research into atropisomers featuring an N-containing axis (N-X atropisomers) remains in its infancy compared with the well-developed C-C atropisomer analogue. Notably, N-X atropisomers could offer divergent scaffolds, which are extremely important in bioactive molecules. The asymmetric synthesis of N-X atropisomers is recognized as both appealing and challenging. Recently, we devoted our efforts to the catalytic asymmetric synthesis of N-X atropisomers, benzimidazole-aryl N-C atropisomers, indole-aryl N-C atropisomers, hydrogen-bond-assisted N-C atropisomers, pyrrole-pyrrole N-N atropisomers, pyrrole-indole N-N atropisomers, and indole-indole N-N atropisomers. To obtain the N-C atropisomers, an asymmetric Buchwald-Hartwig reaction of amidines or enamines was employed. Using a Pd(OAc)2/(S)-BINAP or Pd(OAc)2/(S)-Xyl-BINAP catalyst system, benzimidazole-aryl N-C atropisomers and indole-aryl N-C atropisomers were readily obtained. To address the issue of the reduced stability of the diarylamine axis, a six-membered intramolecular N-H-O hydrogen bond was introduced into the N-C atropisomer scaffold. A tandem N-arylation/oxidation process was used for the chiral phosphoric acid (CPA)-catalyzed asymmetric synthesis of N-aryl quinone atropisomers. For N-N atropisomers, a copper-mediated asymmetric Friedel-Crafts alkylation/arylation reaction was developed. The desymmetrization process was completed successfully via a Cu(OTf)2/chiral bisoxazoline or (CuOTf)·Tol/bis(phosphine) dioxide system, thereby achieving the first catalytic asymmetric synthesis of N/N bipyrrole atropisomers. Asymmetric Buchwald-Hartwig amination of enamines was utilized to provide N-N bisindole atropisomers with excellent stereogenic control. This was the first asymmetric synthesis of N-N atropisomers featuring a bisindole structural scaffold using the de novo indole construction strategy. The asymmetric N-N heterobiaryl atropisomer synthesis was substantially facilitated using palladium-catalyzed transient directing group (TDG)-mediated C-H functionalization. Atropisomeric alkenylation, allylation, or alkynylation was accomplished using the Pd(OAc)2/l-tert-leucine system. Herein, we summarize our work on the palladium-, copper-, and CPA-catalyzed asymmetric syntheses of N-C and N-N atropisomers. Furthermore, the application of our work in the synthesis of bioactive molecule analogues and axially chiral ligands is demonstrated. Subsequently, the stability of the chiral N-containing axis is briefly discussed in terms of single crystals and obtained rotational barriers. Finally, an outlook on the asymmetric N-X atropisomer synthesis is provided.

Molecular Recognition of Aromatics in Spherical Nanocages.

In general, due to the lack of efficient specific molecular interactions, achieving host-guest molecular recognition inside large and neutral metal organic cages (MOCs) is challenging. Preferential molecular recognition of aromatics using the internal binding sites of interlocked icosahedral (i.e., spherical) M12L8MOCs within poly-[n]-catenane (1) is reported. The guest absorption has been monitored directly in the solid-state by consecutive single-crystal-to-single-crystal (SCSC) reactions in a gas-solid environment, using single-crystal X-ray diffraction (SC-XRD) experiments. The preferential guest uptake is corroborated by Density Functional Theory (DFT) calculations by determining the host-guest interaction energy (Ehost-guest) with the nitrobenzene (NB) >> p-xylene (p-xy) >> o-dichlorobenzene (o-DCB) trend (i.e., from 44 kcal/mol to 25 kcal/mol), assessing the XRD outcomes. Combining SC-XRD, DFT and solid-state 13C NMR, the exceptional stability of the M12L8 cages, together with the guest exchange/release properties are rationalized by the presence of mechanical bonds (efficient π-π interactions) and by the pyridine's rotor-like behaviour (with 3 kcal/mol rotational energy barrier). The structure-function properties of M12L8 makes 1 a potential candidate in the field of molecular sensors.

Synthesis, structural analysis, and properties of highly twisted alkenes 13,13’-bis(dibenzo[a,i]fluorenylidene) and its derivatives

The rotation of a C = C bond in an alkene can be efficiently accelerated by creating the high-strain ground state and stabilizing the transition state of the process. Herein, the synthesis, structures, and properties of several highly twisted alkenes are comprehensively explored. A facile and practical synthetic approach to target molecules is developed. The twist angles and lengths of the central C = C bonds in these molecules are 36–58° and 1.40–1.43 Å, respectively, and confirmed by X-ray crystallography and DFT calculations. A quasi-planar molecular half with the π-extended substituents delivers a shallow rotational barrier (down to 2.35 kcal/mol), indicating that the rotation of the C = C bond is as facile as that of the aryl-aryl bond in 2-flourobiphenyl. Other versatile and unique properties of the studied compounds include a broad photoabsorption range (from 250 up to 1100 nm), a reduced HOMO-LUMO gap (1.26–1.68 eV), and a small singlet-triplet energy gap (3.65–5.68 kcal/mol).

Suppressing trap density and energy loss via skeleton asymmetry strategy enables highly efficient all-small-molecule organic solar cells

Reducing energy loss while ensuring the required charge collection is of vital importance to high-performance all-small-molecule organic solar cells (SM-OSCs) limited by high trap density (1016 ∼ 1018 cm−3) in bulk heterojunction films. Herein, we show that the trap density in SM-OSCs can be dramatically reduced by designing a small-molecule donor (SMD) using a skeleton asymmetry strategy. Compared with its symmetric counterpart, TBD-BCl with an asymmetric thienobenzodithiophene (TBD) central core has different rotational energy barriers and a transformed C-shaped configuration, endowing blend films with strong intermolecular interactions and higher crystallinity. Thus, blending TBD-BCl with the L8-BO acceptor leads to a low trap density of 3.21 × 1015 cm−3 and density of state of 46 meV relative to BDT-BCl:L8-BO films. In addition, joint experimental and theoretical studies revealed that the TBD-BCl:L8-BO complex with a much lower driving force can still facilitate exciton dissociation, suppress charge-carrier recombination, and significantly reduce energy loss in devices. As a result, SM-OSCs based on TBD-BCl:L8-BO deliver a higher efficiency of 16.2% and an improved Voc of 0.91 V. Overall, the experiments and theory calculations in this study provide a new perspective for designing SMDs that suppress trap states and reduce the energy loss in SM-OSCs.

3-Ferrocenyl-estra-1,3,5 (10)-triene-17-one: Synthesis, Crystal Structure, Hirshfeld Surface Analysis, DFT Studies, and Its Binding to Human Serum Albumin Studied through Fluorescence Quenching and In Silico Docking Studies.

3-ferrocenyl-estra-1,3,5 (10)-triene-17-one (2), [Fe(C5H5)(C24H25O3)], crystallizes in the monoclinic space group C2. The cyclopentadienyl (Cp) rings adopt a nearly eclipsed conformation, and the Cp plane is tilted by 87.66° with respect to the substituted phenyl plane. An average Fe-C(Cp) bond length of 2.040(13) Å was determined, similar to the one reported for ferrocene. Hirshfeld surfaces and two-dimensional fingerprint plots were generated to analyze weak intermolecular C-H···π and C-H···O interactions. Density functional theory studies revealed a 1.15 kcal/mol rotational barrier for the C3-O1 single bound. Fluorescence quenching studies and in silico docking studies suggest that human serum albumin forms a complex with 2 via a static mechanism dominated by van der Waals interactions and hydrogen bonding interactions.

Theoretical Insights into Aggregation-Induced Emission with the Ionic π Fluorophore: The Importance of Choosing the Dimer QM Model in the ONIOM Study.

In understanding the mechanism of aggregation-induced emission (AIE), the multilevel ONIOM framework has been demonstrated as one of the efficient tools that can capture the essential mechanistic information by choosing a single fluorophore as the quantum mechanics (QM) model and putting all surrounding molecules in the low-level region. Recently, the ionic styryl-pyridine salt (namely, SPH) has been reported as a new class of AIEgen with a high fluorescence yield. In the SPH crystal, a pair of ionic SPH molecules are closely stacked with each other in an antiparallel, head-to-tail pattern, thus the choice of QM models (an individual or dimeric structure) becomes critical in the ONIOM study. Herein we report the AIE mechanism of the ionic SPH at the QM ((TD)-CAM-B3LYP) and ONIOM(QM:MM) levels. As usual, the fluorescence quenching of SPH in tetrahydrofuran (THF) solution is attributed to a nonradiative relaxation via the central C═C bond rotation, with a rather low barrier of 2.7 kcal/mol. In crystals, either with a monomer or dimer model, the fluorescence quenching channel is found to be restricted due to the obvious C═C rotation barriers. Compared with the monomer model, the dimer model, by treating the orbital interaction of the two SPH molecules at the QM level, provides significantly increased barriers and a red-shifted emission wavelength that better matches the experimental value. In addition, the calculated exciton coupling in the fluorescence emission state can be discovered only by a dimer model. The findings here emphasize not only the importance of choosing a proper model in the ONIOM study of AIE but also expanding our understanding of novel AIE systems.

Modulation of Rotational Dynamics in Halogen-Bonded Cocrystalline Solids.

Dynamic processes are responsible for the functionality of a range of materials, biomolecules, and catalysts. We report a detailed systematic study of the modulation of methyl rotational dynamics via the direct and the indirect influence of noncovalent halogen bonds. For this purpose, a novel series of cocrystalline architectures featuring halogen bonds (XB) to tetramethylpyrazine (TMP) is designed and prepared using gas-phase, solution, and solid-state mechanochemical methods. Single-crystal X-ray diffraction reveals the capacity of molecular bromine as well as weak chloro-XB donors to act as robust directional structure-directing elements. Methyl rotational barriers (Ea) measured using variable-temperature deuterium solid-state NMR range from 3.75 ± 0.04 kJ mol-1 in 1,3,5-trichloro-2,4,6-trifluorobenzene·TMP to 7.08 ± 0.15 kJ mol-1 in 1,4-dichlorotetrafluorobenzene·TMP. Ea data for a larger series of TMP cocrystals featuring chloro-, bromo-, and iodo-XB donors are shown to be governed by a combination of steric and electronic factors. The average number of carbon-carbon close contacts to the methyl group is found to be a key steric metric capable of rationalizing the observed trends within each of the Cl, Br, and I series. Differences between each series are accounted for by considering the strength of the σ-hole on the XB donor. One possible route to modulating dynamics is therefore via designer cocrystals of variable stoichiometry, maintaining the core chemical features of interest between a given donor and acceptor while simultaneously modifying the number of carbon close contacts affecting dynamics. These principles may provide design opportunities to modulate more complex geared or cascade dynamics involving larger functional groups.

Benzothiadiazole-based rotation and possible antipolar order in carboxylate-based metal-organic frameworks

By modifying organic ligands of metal-organic framework with dipolar units, they turn suitable for various applications, e.g., in the field of sensor systems or switching of gas permeation. Dipolar linkers in the organic ligand are capable to rotate in certain temperature and frequency ranges. The copper-bearing paddlewheel shaped metal-organic frameworks ZJNU-40 and JLU-Liu30 possess such a polarizable dipole moment due to their benzothiadiazole moiety in the organic ligands. Here, we investigate the molecular rotor behavior of benzothiadiazole units of the two carboxylate-based MOFs by dielectric spectroscopy and computational simulation. Our dielectric results provide clear evidence for significant reorientational relaxation dynamics of these rotors, revealing various characteristics of glasslike freezing upon cooling. The calculated rotational energy barriers are consistent with experimentally determined barriers for single-dipole dynamics. Moreover, for JLU-Liu30 we find hints at antipolar ordering below about 300 K.

Atroposelective Brønsted Acid-Catalyzed Photocyclization to Access Chiral N-Aryl Quinolones with Low Rotational Barriers.

Herein, a novel route to atropisomeric N-aryl quinolones with low rotational barriers is demonstrated, leveraging a dual photochemical/organocatalytic approach to the required ring closure in up to 94% yield and up to >99% ee. The use of a continuous flow system allows for impurity suppression and enables rapid scale-up to a decagram scale.

Construction of C-B axial chirality via dynamic kinetic asymmetric cross-coupling mediated by tetracoordinate boron.

Catalytic dynamic kinetic asymmetric transformation (DyKAT) provides a powerful tool to access chiral stereoisomers from racemic substrates. Such transformation has been widely employed on the construction of central chirality, however, the application in axial chirality remains underexplored because its equilibrium of substrate enantiomers is limited to five-membered metalacyclic intermediate. Here we report a tetracoordinate boron-directed dynamic kinetic asymmetric cross-coupling of racemic, configurationally stable 3-bromo-2,1-azaborines with boronic acid derivatives. A series of challenging C-B axially chiral compounds were prepared with generally good to excellent enantioselectivities. Moreover, this transformation can also be extended to prepare atropisomers bearing adjacent C-B and C-C diaxes with excellent diastereo- and enantio-control. The key to the success relies on the rational design of a reversible tetracoordinate boron intermediate, which is supported by theoretical calculations that dramatically reduces the rotational barrier of the original C-B axis and achieves the goal of DyKAT.

Diffusion of small anti-Schottky clusters in UO2

The aggregation of irradiation-induced defect clusters in UO2 leads to the formation of dislocation loops and cavities which contribute swelling and ultimately produce deleterious effects on the fuel. Despite their fundamental role in fuel evolution, the kinetics of these defect clusters are not currently well understood. In this work, we investigate the diffusive behavior of interstitial clusters via Molecular Dynamics (MD) simulations. Our investigation considers a range of defect cluster sizes, each composed of N UO2 units or anti-Schottky defects. We report a complex cluster size - mobility relation; increasing cluster size corresponds to an increase in mobility up until a critical size (N=4) where diffusivity reaches a maximum, after which the trend reverts and further increasing size corresponds to a decrease in mobility. The rapid migration observed correlates well with the very low barriers reported in a few historic experimental studies. Further analysis of the cluster shape and orientation reveals a strong structural preference for near-planar configurations oriented normal to the 〈100〉 direction. Rotational energy barriers are found to be similar in both magnitude and trend to the observed diffusion barriers. Lastly, connections are drawn to the behavior of large defect clusters including the formation of (1/3)〈111〉 Frank dislocation loops.

H/Br substitution in ethylamine improves the phase transition temperature of in-based material (BrC2H4NH3)3[InBr6

Organic-inorganic hybrid phase transition materials with simple synthesis and flexible structure have become a research hotspot. However, one of the obstacles for expanding their application prospects is how to effectively adjust the phase transition temperature. Herein, taking advantage of H/Br substitution on the reported In-based phase transition material (C2H5NH3)3[InBr6], a new In-based material (BrC2H4NH3)3[InBr6] (1) was successfully prepared (Tc = 288 K). As expected, the Tc is successfully improved from 248 K of (C2H5NH3)3[InBr6] to 288 K of (BrC2H4NH3)3[InBr6], effectively regulating the phase transition temperature. The variable-temperature structure elucidation suggests that the disorder degree transitions of (BrC2H4NH3)+ cations triggers the phase transition. The introduction of heavier atom (Br) and Br···Br interaction increases the rotational energy barrier of the (BrC2H4NH3)+ cation, which leads to the enhancement of the phase transition temperature. In addition, compound 1 shows dielectric anomalies near Tc, which is consistent with DSC result. This work provides an effective method for further expanding the application range of phase transition materials.

PhysNet meets CHARMM: A framework for routine machine learning/molecular mechanics simulations.

Full-dimensional potential energy surfaces (PESs) based on machine learning (ML) techniques provide a means for accurate and efficient molecular simulations in the gas and condensed phase for various experimental observables ranging from spectroscopy to reaction dynamics. Here, the MLpot extension with PhysNet as the ML-based model for a PES is introduced into the newly developed pyCHARMM application programming interface. To illustrate the conception, validation, refining, and use of a typical workflow, para-chloro-phenol is considered as an example. The main focus is on how to approach a concrete problem from a practical perspective and applications to spectroscopic observables and the free energy for the -OH torsion in solution are discussed in detail. For the computed IR spectra in the fingerprint region, the computations for para-chloro-phenol in water are in good qualitative agreement with experiment carried out in CCl4. Moreover, relative intensities are largely consistent with experimental findings. The barrier for rotation of the -OH group increases from ∼3.5 kcal/mol in the gas phase to ∼4.1 kcal/mol from simulations in water due to favorable H-bonding interactions of the -OH group with surrounding water molecules.

Equilibrium structures of selenium compounds: The torsionally flexible molecule of selenophenol.

The equilibrium structure of selenophenol has been investigated using rotational spectroscopy and high-level quantum mechanical calculations, offering electronic and structural insight into the scarcely studied selenium compounds. The jet-cooled broadband microwave spectrum was measured in the 2-8GHz cm-wave region using broadband (chirped-pulse) fast-passage techniques. Additional measurements up to 18GHz used narrow-band impulse excitation. Spectral signatures were obtained for six isotopic species of selenium (80Se, 78Se, 76Se, 82Se, 77Se, and 74Se), together with different monosubstituted 13C species. The (unsplit) rotational transitions associated with the non-inverting μa-dipole selection rules could be partially reproduced with a semirigid rotor model. However, the internal rotation barrier of the selenol group splits the vibrational ground state into two subtorsional levels, doubling the dipole-inverting μb transitions. The simulation of the double-minimum internal rotation gives a very low barrier height (B3PW91: 42cm-1), much smaller than for thiophenol (277cm-1). A monodimensional Hamiltonian then predicts a huge vibrational separation of 72.2GHz, justifying the non-observation of μb transitions in our frequency range. The experimental rotational parameters were compared with different MP2 and density functional theory calculations. The equilibrium structure was determined using several high-level abinitio calculations. A final Born-Oppenheimer (reBO) structure was obtained at the coupled-cluster CCSD(T)_ae/cc-wCVTZ level of theory, including small corrections for the wCVTZ → wCVQZ basis set enlargement calculated at the MP2 level. The mass-dependent method with predicates was used to produce an alternative rm(2) structure. The comparison between the two methods confirms the high accuracy of the reBO structure and offers information on other chalcogen-containing molecules.

Molecular Dynamics Simulations of High-Concentration Li[TFSA] Sulfone Solution: Effect of Easy Conformation Change of Sulfolane on Fast Diffusion of Li Ion.

The parameters of the polarizable force field used for molecular dynamics simulations of Li diffusion in high-concentration lithium bis(trifluoromethanesulfonyl)amide (Li[TFSA]) sulfone (sulfolane, dimethylsulfone, ethylmethylsulfone, and ethyl-i-propylsulfone) solutions were refined. The densities of the solutions obtained by molecular dynamics simulations reproduced well the experimental values. The calculated concentration, temperature, and solvent dependencies of self-diffusion coefficients of ions and solvents in the mixtures well reproduce the experimentally observed dependencies. Ab initio calculations show that the intermolecular interactions between Li ions and four sulfones are not largely different. Conformational analyses show that sulfolane can change the conformation more easily owing to lower barrier height for pseudorotation compared to the rotational barrier heights of diethylsulfone and ethylmethylsulfone. Molecular dynamics simulations indicate that the easy conformation change of solvent affects the rotational relaxation of the solvent and the diffusion of Li ion in the mixture. The easy conformation change of sulfolane is one of the causes of faster diffusion of Li ion in the mixture of Li[TFSA] and sulfolane compared to the mixtures of smaller dimethylsulfone and ethylmethylsulfone.

Exploring the Stability and Disorder in the Polymorphs of L-Cysteine through Density Functional Theory and Vibrational Spectroscopy.

Static and dynamic density functional calculations are reported for the four known polymorphs of l-cysteine. Static calculations are used to explore the relative free energies (within the harmonic approximation) of the polymorphs as a function of pressure. An important feature of the structural differences between the polymorphs is shown to be the dihedral angle of the C-C-S-H bond. It is shown that, by varying this angle, it is possible to move between hydrogen bonding motifs S-H···S and S-H···O in all four polymorphs. The energetics for dihedral angle rotation are explored, and the barriers for rotation between the hydrogen bonding motifs have been calculated for each polymorph. Two possible models for the experimental disorder observed in Form I at room temperature are explored using both static and dynamic methods; a domain disorder model, where the disorder is localized, and a dispersed disorder model, where the disorder is randomly distributed throughout the crystal. Molecular dynamics calculations show transitions between the two hydrogen bonding motifs occurring in the dispersed disorder model at 300 and 350 K. In addition, molecular dynamics calculations of Form IV also showed the onset of hydrogen bond disorder at 300 K. Calculations of the predicted infrared and terahertz absorption are performed for both the static and dynamic simulations, and the results are compared with experimental results to understand the influence of disorder on the observed spectra.

Diaryl-Pyrano-Chromenes Atropisomers: Stereodynamics and Conformational Studies.

The dynamic scenario of di-aryls-pyrano-chromenes was investigated using DFT calculations. The symmetry of the chromene scaffold and the presence of two ortho-substituted aryls substituents can generate two syn/anti diastereoisomers and conformational enantiomers with different rotational barriers. The relative conformations and configurations were derived using NOESY-1D experiments. Depending on the energies related to the conformational exchange, the experimental energy barriers were determined through Dynamic NMR, Dynamic HPLC or kinetic studies. The atropisomeric pairs were resolved in the latter scenario, and their absolute configuration was assigned using the ECD/TD-DFT method.

N-Heterocyclic Carbene-Catalyzed Atroposelective Synthesis of N–N Axially Chiral 3-Amino Quinazolinones

Although the atroposelective synthesis of biaryls and related compounds bearing axially chiral C–C bonds is well-known, the synthesis of axially chiral C–N bond-containing compounds is relatively less explored, and the construction of axially chiral N–N bonds has received only scant attention. Demonstrated herein is the N-heterocyclic carbene (NHC)-catalyzed selective amidation reaction, leading to the atroposelective synthesis of N–N axially chiral 3-amino quinazolinones. The NHC-catalyzed reaction of quinazolinones containing a free N–H moiety with α,β-unsaturated aldehydes under oxidative conditions furnished the atropisomeric quinazolinone derivatives under mild conditions and broad scope. Preliminary studies on experimental and density functional theory-based N–N rotational barrier determination are also presented.

Intramolecular noncovalent interactions in bis-imidazolium dications with short aliphatic spacers

Stretched all-trans conformations were found preferable in computed structures of bis-imidazolium dications with short aliphatic (С1-С4) and hydroxyl substituted -СН2-СНОН-СН2- spacers. Maxima of molecular electrostatic potential were established near С2Н imidazolium and spacer hydrogens, for α,ω-alkenyl spacers, and close to hydroxyl hydrogen for hydroxypropane spacer. Sufficiently higher rotational barrier around С1-C2 bond in -СН2-СНОН-СН2- spacer compared with polymethylene is supported with intramolecular hydrogen bonds С-Н···О-Н between imidazolium hydrogens and hydroxyl oxygen.

The rotational movement in solution of fumaramide- vs. succinamide [2]rotaxanes: The influence of intercomponent interactions

Due to their intrinsic topological features, most artificial molecular devices are based on rotaxane molecules. One of the most important characteristics of this class of compounds is the likelihood of performing molecular movements, which are directly correlated with the intercomponent interactions present in these molecules. The tetralactam macrocycle is quite versatile and used in numerous molecular threads, which have stations that work as fundamental parts in the formation, molecular stabilization, and molecular movements performed. Inspired by how these stations may influence molecular movements (e.g., rotational ones), we sought to study two diamides commonly used as rotaxane stations: fumaramide and succinamide. In this context, we explored the change of station in six pairs of [2]rotaxanes. Studies were carried out in solution through NMR experiments with temperature variation techniques. In the crystalline solid state, the quantum theory of atoms in molecules analysis was performed through quantum mechanics calculations using the density functional theory. The rotational movement found for fumaramide-based [2]rotaxanes is, on average, over 14.91 kcal mol−1. In comparison, succinamide-based [2]rotaxanes have values of 12.78 kcal mol−1 (a 14% difference). In solution, fumadamide-based rotaxanes better retain the macrocycle due to the rigidity of the double bond, making its rotation more difficult and consequently leading to higher rotational energy barriers. In the crystalline solid state, the succinamide station, which has greater structural freedom due to the simple carbon–carbon bond, promotes more interactions, having a greater “complementary adjustment” and a higher stabilization energy. Lastly, our findings demonstrated how intercomponent interactions present in the studied stations can be changed to be used as a “lubricant” in solution for these molecular machine prototypes.