Absolute Configuration of Small Molecules by Co-Crystallization

The most reliable method to determine the absolute configuration of chiral molecules is X-ray crystallography, but small molecules can be difficult to crystallize. We report rapid co-crystallization of tetraaryladamantanes with small molecules as different as n-decane to nicotine to produce crystals for X-ray analysis and the assignment of absolute configuration when the molecules are chiral. A screen of 52 diverse compounds gave inclusion in co-crystals for 88 % of all cases and a high-resolution structure in 77 % of cases. Furthermore, starting from three milligrams of analyte, a combination of NMR spectroscopy and X-ray crystallography produced a full structure in less than three days using an adamantane crystallization chaperone that encapsulates the analyte at room temperature.     

Polymorphism of N,N'-diacetylbiuret studied by solid-state 13C and 15N NMR spectroscopy, DFT calculations, and X-ray diffraction

The molecular configuration and crystal structure of solid polycrystalline N,N′′‐diacetylbiuret (DAB), a potential nitrogen‐rich fertilizer, have been analyzed by a combination of solid‐ and liquid‐state NMR spectroscopy, X‐ray diffraction, and DFT calculations. Initially a pure NMR study (“NMR crystallography”) was performed as available single crystals of DAB were not suitable for X‐ray diffraction. Solid‐state ¹³C NMR spectra revealed the unexpected existence of two polymorphic modifications (α‐ and β‐DAB) obtained from different chemical procedures. Several NMR techniques were applied for a thorough characterization of the molecular system, revealing chemical shift anisotropy (CSA) tensors of selected nuclei in the solid state, chemical shifts in the liquid state, and molecular dynamics in the solid state. Dynamic NMR spectroscopy of DAB in solution revealed exchange between two different configurations, which raised the question, is there a correlation between the two different configurations found in solution and the two polymorphic modifications found in the solid state? By using this knowledge, a new crystallization protocol was devised which led to the growth of single crystals suitable for X‐ray diffraction. The X‐ray data showed that the same symmetric configuration is present in both polymorphic modifications, but the packing patterns in the crystals are different. In both cases hydrogen bonds lead to the formation of planes of DAB molecules. Additional symmetry elements, a two‐fold screw in the case of α‐DAB and a c‐glide plane in the case of β‐DAB, lead to a more symmetric (α‐DAB) or asymmetric (β‐DAB) intermolecular hydrogen‐bonding pattern for each molecule.     

Synthesis and structure elucidation of a series of pyranochromene chalcones and flavanones using 1D and 2D NMR spectroscopy and X‐ray crystallography

A series of novel pyranochromene chalcones and corresponding flavanones were synthesized. This is the first report on the confirmation of the absolute configuration of chromene‐based flavanones using X‐ray crystallography. These compounds were characterized by 2D NMR spectroscopy, and their assignments are reported herein. The 3D structure of the chalcone 3b and flavanone 4g was determined by X‐ray crystallography, and the structure of the flavanone was confirmed to be in the S configuration at C‐2. Copyright © 2014 John Wiley & Sons, Ltd.     

Circularly Polarized Luminescence of Aluminum Complexes for Chiral Sensing of Amino Acid and Amino Alcohol

Determination of the absolute configuration (AC) of chiral molecules is a key issue in many fields related to chirality such as drug development, the asymmetric reaction screening, and the structure determination of natural compounds. Although various methods, such as X‐ray crystallography and NMR spectroscopy, are used to determine the AC, a simple and cheap alternative method is always anticipated. So far, electronic circular dichroism (ECD) spectroscopy has been widely used to ascertain the AC and enantiomeric excess (ee) values by applying appropriate organic probes. Here, circularly polarized luminescence (CPL) spectroscopy was applied to determine the AC and ee values of a series of amino acid and amino alcohol. The measurements were conducted by mixing the amino acids or amino alcohols with an achiral 1‐hydroxy‐2‐naphthaldehyde. Upon in situ formation of the Schiff base complexes, the system showed emission enhancement and CPL in the presence of Al³⁺, whose intensity and sign can be used to assign the chiral sense of the amino acids and amino alcohols. The authenticity of the method was further compared with the established CD spectroscopy, revealing that CPL spectra of formed Al³⁺ complex were effective to determine the AC of chiral species.     

Quantum crystallography: A perspective

Extraction of the complete quantum mechanics from X‐ray scattering data is the ultimate goal of quantum crystallography. This article delivers a perspective for that possibility. It is desirable to have a method for the conversion of X‐ray diffraction data into an electron density that reflects the antisymmetry of an N‐electron wave function. A formalism for this was developed early on for the determination of a constrained idempotent one‐body density matrix. The formalism ensures pure‐state N‐representability in the single determinant sense. Applications to crystals show that quantum mechanical density matrices of large molecules can be extracted from X‐ray scattering data by implementing a fragmentation method termed the kernel energy method (KEM). It is shown how KEM can be used within the context of quantum crystallography to derive quantum mechanical properties of biological molecules (with low data‐to‐parameters ratio). © 2017 Wiley Periodicals, Inc.     

Absolute Configuration from Different Multifragmentation Pathways in Light‐Induced Coulomb Explosion Imaging

The absolute configuration of individual small molecules in the gas phase can be determined directly by light‐induced Coulomb explosion imaging (CEI). Herein, this approach is demonstrated for ionization with a single X‐ray photon from a synchrotron light source, leading to enhanced efficiency and faster fragmentation as compared to previous experiments with a femtosecond laser. In addition, it is shown that even incomplete fragmentation pathways of individual molecules from a racemic CHBrClF sample can give access to the absolute configuration in CEI. This leads to a significant increase of the applicability of the method as compared to the previously reported complete break‐up into atomic ions and can pave the way for routine stereochemical analysis of larger chiral molecules by light‐induced CEI.     

Configurationally Stable Chiral Dithia‐Bridged Hetero[4]helicene Radical Cation: Electronic Structure and Absolute Configuration

A stable chiral hetero[4]helicene radical cation was synthesized and characterized by UV/Vis absorption and EPR spectroscopy, as well as X‐ray crystallography. For the first time, a combination of chiroptical methods involving ECD, ORD, and VCD, supported by quantum mechanical predictions, enabled the elucidation of the absolute configuration of such open‐shell helical species.     

From an α‐Functionalized Silicon‐Stereogenic N,O‐Silane to a Monomeric and Tetracoordinate tBuLi Adduct with Lithium‐Centered Chirality

Donor‐functionalized silanes with stereogenic silicon centers are extremely rare. A convenient stereocontrolled route to a nitrogen‐oxygen‐functionalized silicon‐chiral compound with an additional aminomethyl function is presented. This silane was directly achieved in stereochemically pure form by a simple nucleophilic substitution reaction. Owing to the unique asymmetry of this silane and the presence of three donor functions, the first monomeric butyllithium compound with lithium‐centered chirality could be isolated; the configuration was assigned by X‐ray crystallography. This [silane? tBuLi] complex undergoes an unexpected deprotonation/stereospecific substitution sequence in toluene, leading to the development of a convenient one‐pot synthesis of a functionalized silicon‐chiral benzylsilane, which proceeds with inversion of configuration and complete preservation of the stereochemical integrity at silicon.     

Versatile Syntheses of Hemi‐Cryptophanes and a Metallo‐Cryptophane from a Hexa‐Functionalized C3v‐Symmetrical Tribenzotriquinacene (TBTQ) Derivative

A number of three‐fold C_3v‐symmetrical tribenzotriquinacene (TBTQ) cavitands were synthesized by a “metamorphosis‐to‐half” strategy, employing six‐fold etherification reactions between the hexakis(chloromethyl)‐TBTQ intermediate 2 a and various 5‐functionalized resorcinols. X‐ray structure analyses of single crystals of the cavitands revealed limited rotational flexibility of the resorcinol bridging units, which enables an apical, nearly co‐axial orientation of the three functional groups and, as a consequence, the construction of nanoscale cage‐like molecules via covalent or coordination bonding. On this basis, two TBTQ‐based hemicryptophanes were prepared from the TBTQ cavitands via covalent bond formation in good yields. A dumbbell‐shaped TBTQ‐based metallo‐cryptophane was also synthesized in 34 % yield by a solvothermal reaction between cadmium nitrate and two equivalents of the TBTQ‐cavitand triacid, as confirmed by single‐crystal X‐ray diffraction and MALDI‐ToF mass spectrometry.     

A Mild and Highly Efficient Synthesis of Chiral N‐Dichloroacetyl‐4‐ethyl‐1,3‐oxazolidines

Chiral 2‐amino‐butanols ( 4 and 5 ) were obtained via the isolation of diastereomeric salt. Then, chiral compounds ( 6 – 9) were synthesized by a sequential procedure involving condensation of chiral 2‐amino‐butanol with ketone and dichloroacetyl chloride. All the compounds were characterized by IR, ¹H NMR, ¹³C NMR, and element analysis. The absolute configurations of ( S )‐ 8 was determined by X‐ray crystallography.     

A New Approach to Enantiopure C3‐Symmetric Molecules

Chiral base chemistry has been used to create three chiral centres in one pot on a C₃‐symmetric substrate. The potential of this new approach to C₃‐symmetric molecules is exemplified by the creation of an enantiopure C_3v‐symmetric triol, triphosphane and tripyridine. A ruthenium complex of the last compound has been studied by X‐ray crystallography.     

The truth about false unicorn (Chamaelirium luteum): total synthesis of 23R,24S-chiograsterol B defines the structure and stereochemistry of the major saponins from this medicinal herb

Chamaelirium luteum is used in traditional medicine systems and commercial botanical dietary supplements for the treatment of female reproductive health problems. Despite the wide use of this herb, only very limited phytochemical characterisation is available. Our investigation of C. luteum roots led to the isolation of two new steroidal saponins 1 and 2 that contain an unusual aglycone 3 . The absolute configurations of these molecules were unable to be determined spectroscopically and thus the total synthesis of 3 was undertaken and achieved in 16 steps and 1.6 % overall yield from pregnenolone. The key step in the synthesis was the stereoselective installation of the side chain at C‐17 and C‐20, which employed anion‐accelerated oxy‐Cope methodology. The relative configuration of aglycone 3 was determined by X‐ray crystallography of an advanced synthetic intermediate. The absolute configuration was based upon that of the pregnenolone‐derived steroidal skeleton and determined to be 23R,24S.     

Enantiopure Functional Molecular Motors Obtained by a Switchable Chiral‐Resolution Process

Molecular switches, rotors, and motors play an important role in the development of nano‐machines and devices, as well as responsive and adaptive functional materials. For unidirectional rotors based on chiral overcrowded alkenes, their stereochemical homogeneity is of crucial importance. Herein, a method to obtain new and functionalizable overcrowded alkenes in enantiopure form is presented. The procedure involves a short synthesis of three steps and a solvent‐switchable chiral resolution by using a readily available resolving agent. X‐ray crystallography revealed the mode of binding of the motor with the resolving agent, as well as the absolute configuration of the motor. ¹H NMR and UV/Vis spectroscopy techniques were used to determine the dynamic behavior of this molecular motor. This method provides rapid access to ample amounts of enantiopure molecular motors, which will greatly facilitate the further development of responsive molecular systems based on chiral overcrowded alkenes.     

HUG and SQUEEZE: using CRYSTALS to incorporate resonant scattering in the SQUEEZE structure‐factor contributions to determine absolute structure

The resonant‐scattering contributions to single‐crystal X‐ray diffraction data enable the absolute structure of crystalline materials to be determined. Crystal structures can be determined even if they contain considerably disordered regions because a correction is available via a discrete Fourier transform of the residual electron density to approximate the X‐ray scattering from the disordered region. However, the corrected model cannot normally account for resonant scattering from atoms in the disordered region. Straightforward determination of absolute structure from crystals where the strongly resonantly scattering atoms are not resolved has therefore not been possible. Using an approximate resonant‐scattering correction to the X‐ray scattering from the disordered regions, we have developed and tested a procedure (HUG) to recover the absolute structure using conventional Flack x refinement or other post‐refinement determination methods. Results show that in favourable cases the HUG method works well and the absolute structure can be correctly determined. It offers no useful improvement in cases where the original correction for the disordered region scattering density is problematic, for example, when a large fraction of the scattering density in the crystal is disordered, or when voids are not occupied equally by the disordered species. Crucially, however, if the approach does not work for a given structure, the statistics for the absolute structure measures are not improved, meaning it is unlikely to lead to misassignment of absolute structure.     

Synthesis of Diastereoenriched α‐Aminomethyl Enaminones via a Brønsted Acid‐Catalyzed Asymmetric aza‐Baylis‐Hillman Reaction of Chiral N‐Phosphonyl Imines

An effective chiral GAP methodology for preparing α‐aminomethyl enaminones through a (R)‐CSA‐catalyzed asymmetric aza‐Baylis‐Hillman reaction is reported. Excellent yields and high diastereoselectivity could be obtained under mild conditions and convenient GAP techniques. The confirmations of the absolute configuration of N‐phosphonyl imine and chiral enaminone by X‐ray diffraction provides an explicit explanation of the chirality mechanism for GAP chemistry.     

Ab initio X‐ray structural characterization of an inclusion compound with a compositionally disordered chiral guest: no prior knowledge of the crystal composition

The crystal structure and absolute configuration of a molecular host/guest/impurity inclusion complex were established unequivocally in spite of our having no prior knowledge of its chemical composition. The host (4R,5R)‐4,5‐bis(hydroxydiphenylmethyl)‐2,2‐dimethyl‐1,3‐dioxolane, (I), displays expected conformational features. The crystal‐disordered chiral guest 4,4a,5,6,7,8‐hexahydronaphthalen‐2(3H)‐one, (II), is present in the crystal 85.1 (4)% of the time. It shares a common site with 4a‐hydroperoxymethyl‐4,4a,5,6,7,8‐hexahydronaphthalen‐2(3H)‐one, (III), present 14.9 (4)% of the time, which is the product of autoxidation of (II). This minor peroxide impurity was isolated, and the results of nuclear magnetic resonance, mass spectrometry, and X‐ray fluorescence studies are consistent with the proposed structure of (III). The complete structure was therefore determined to be (4R,5R)‐4,5‐bis(hydroxydiphenylmethyl)‐2,2‐dimethyl‐1,3‐dioxolane–4,4a,5,6,7,8‐hexahydronaphthalen‐2(3H)‐one–4a‐hydroperoxymethyl‐4,4a,5,6,7,8‐hexahydronaphthalen‐2(3H)‐one (1/0.85/0.15), C₃₁H₃₀O₄·0.85C₁₀H₁₄O·0.15C₁₀H₁₄O₃, (IV). There are host–host, host–guest, and host–impurity hydrogen‐bonding interactions of types S and D in the solid state. We believe that the crystals of (IV) were originally prepared to establish the chirality of the guest (II) by means of X‐ray diffraction analysis of host/guest crystals obtained in the course of chiral resolution during cocrystallization of (II) with (I). In spite of the absence of `heavy' elements, the absolute configurations of all anomeric centres in the structure are assigned as R based on resonant scattering effects.     

Chiral Encapsulation by Directional Interactions

The complexation of chiral guests in the cavity of dimeric self‐assembled chiral capsule 1 ₂ was studied by using NMR spectroscopy and X‐ray crystallography. Capsule 1 ₂ has walls composed of amino acid backbones forming numerous directional binding sites that are arranged in a chiral manner. The polar character of the interior dictates the encapsulation preferences towards hydrophilic guests and the ability of the capsule to extract guests from water into an organic phase. Chiral discrimination towards hydroxy acids was evaluated by using association constants and competition experiments, and moderate de values were observed (up to 59 %). Complexes with one or two guest molecules in the cavity were formed. For 1:1 complexes, solvent molecules are coencapsulated; this influences guest dynamics and makes the chiral recognition solvent dependent. Reversal of the preferences can be induced by coencapsulation of a nonchiral solvent in the chiral internal environment. For complexes with two guests, filling of the capsule’s internal space can be very effective and packing coefficients of up to 70 % can be reached. The X‐ray crystal structure of complex 1 ₂?((S) ‐6 )₂ with well‐resolved guest molecules reveals a recognition motif that is based on an extensive system of hydrogen bonds. The optimal arrangement of interactions with the alternating positively and negatively charged groups of the capsule’s walls is fulfilled by the guest carboxylic groups acting simultaneously as hydrogen‐bond donors and acceptors. An additional guest molecule interacting externally with the capsule reveals a possible entrance mechanism involving a polar gate. In solution, the structural features and dynamic behavior of the D₄‐symmetric homochiral capsule were analyzed by variable‐temperature NMR spectroscopy and the results were compared with those for the S₈‐symmetric heterochiral capsule.     

Versatile Switching in Substrate Topicity: Supramolecular Chirality Induction in Di‐ and Trinuclear Host Complexes

Supramolecular chirality effects have been achieved both for ditopic and monotopic substrates by using a programmable bis‐salphen scaffold that incorporates either two or three Zn nuclei. The dinuclear host shows preferential chirogenesis in the presence of ditopic systems, whereas effective chirality transfer to the trinuclear complex is realized through monotopic binding. The mode of binding in the trinuclear host has been investigated through X‐ray crystallography, CD measurements, UV/Vis spectroscopy, and DFT analysis. The bis‐salphen scaffold holds promise for the development of substrate‐specific host systems useful for determination of the absolute configuration of various types of organic molecules.     

The influence of short chain branch on formation of shish‐kebab crystals in bimodal polyethylene under shear at high temperatures

Formation of shish‐kebab crystals due to the coil–stretch transition under shear in the molten state using a bimodal polyethylene system with high molecular weight (HMW) fraction having different branch content was investigated. In specific, in situ small‐angle X‐ray scattering (SAXS) and wide‐angle X‐ray diffraction (WAXD) techniques were used to study the structure evolution of shish‐kebab crystals at high temperatures under simple shear. The SAXS results revealed that with the increase of branch content, shish‐kebab crystals became more stable at high temperatures (e.g., 139 °C). However, the shish length of the bimodal PE containing 0.11% branch was shorter than that with no branch. The WAXD results showed that the degree of crystallization for bimodal PE with HMW fraction having 0.11% branch increased with time but reached a plateau value of 1%, while that with no branch increased continuously till 11%. Furthermore, the crystal orientation of bimodal PE with HMW fraction having 0.11% branch was above 0.9 and maintained at a constant value, while that with no branch decreased from 0.9 to 0.1 upon relaxation. This study indicates that even though the crystallizability of the HMW fraction with branch content decreased, they could effectively stabilize the shear‐induced crystalline structure with shorter shish‐kebab crystals. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 786–794     

Influence of chirality on the mesophase of side chain polymers with phenyl benzoate pendant groups

To reveal the structure of an amorphous mesophase with a hidden liquid crystalline structure (ISm*) in a chiral side chain polymer, P8*M, its racemic isomer has been synthesized along with two more RS‐copolymers with controlled enantiomer excess. The phase behaviour of the copolymers was studied comparatively by DSC and X‐ray scattering. Optical rotatory dichroism was measured for thin films of P8*M and two homologue polymers, differing in the polymeric main chain, by the size of the chiral terminal group and by its absolute configuration. A helical superstructure with pitch of about 250?nm is indicated within the ISm* mesophase. Its structure as a short pitch TGB phase hase been proven conclusively.