Crystallization of chiral molecular compounds: what can be learned from the Cambridge Structural Database?

PhAI: A deep-learning approach to solve the crystallographic phase problem

X-ray crystallography provides a distinctive view on the three-dimensional structure of crystals. To reconstruct the electron density map, the complex structure factors [Formula: see text] of a sufficiently large number of diffracted reflections must be known. In a conventional experiment, only the amplitudes [Formula: see text] are obtained, and the phases ϕ are lost. This is the crystallographic phase problem. In this work, we show that a neural network, trained on millions of artificial structure data, can solve the phase problem at a resolution of only 2 angstroms, using only 10 to 20% of the data needed for direct methods. The network works in common space groups and for modest unit-cell dimensions and suggests that neural networks could be used to solve the phase problem in the general case for weakly scattering crystals.

Enantiospecific crystallisation behaviour of malic acid in mechanochemical reactions with vinpocetine

We report an intriguing example of enantioselectivity in the formation of new multicomponent crystalline solid containing vinpocetine and malic acid. Several experimental data sets confirmed that the multicomponent system presents a clear enantiospecific crystallisation behaviour both in the solid-state and in solution: only the system consisting of vinpocetine and L-malic acid produces a free-flowing solid consisting of a new crystalline form, while the experiments with D-malic acid produced an amorphous and often deliquescent material. The new vinpocetine-L-malic system crystallizes in the monoclinic space group of P21 and in a 1:1 molar ratio, where the two molecules are linked through intermolecular hydrogen bonds in the asymmetric unit. The vinpocetine-DL-malic system was partially crystalline (with also traces of unreacted vinpocetine) with diffraction peaks corresponding to those of vinpocetine-L-malic acid. Solid-state NMR experiments revealed strong ionic interactions in all the three systems. However, while vinpocetine-L-malic acid system was a pure and crystalline phase, the other two systems persistently showed the presence of unreacted vinpocetine. This resulted in a significant worsening of the dissolution profile with respect to the pure vinpocetine-L-malic crystalline salt, whose dissolution kinetics appeared superior.

Benzoyl Valine Quasiracemates: Pairing CF3 Quasienantiomers with H to t-Butyl

Understanding the interplay of structural features responsible for molecular assembly is essential for molecular crystal engineering. When assembling molecules with encoded motifs, first choice supramolecular strategies almost always include robust directional nonbonded contacts. Quasiracemic materials, considered near racemates since cocrystallization occurs with chemically unique components, lack a molecular framework or functional group restrictions, highlighting the importance of molecular shape to molecular assembly. Recently, our group reported quasiracemates derived from benzoyl leucine/phenylalanine derivatives with two points of chemical difference. In this study, we modified the chemical framework with valine and increased the scope of the work by imposing a larger variance in the side chain substituents. Pairing a CF3 component with quasienantiomers that differ iteratively from hydrogen to t-butyl offers an important view into the supramolecular landscape of these materials. Single-crystal X-ray crystallography and lattice energy assessments, coupled with conformational and crystal structure similarity searches, show an elevated degree of isomorphism for many of the targeted 17 racemates and quasiracemates. These benzoyl amino acid molecular architectures create extended hydrogen-bond patterns in the crystal that provide enhanced opportunities to study the shape space and molecular recognition profiles for a diverse family of quasienantiomeric components.

Homochiral vs. heterochiral preference in chiral self-recognition of cyclic diols

The structure and clustering propensity of a chiral derivative of cis-1,2-cyclohexanediol, namely, 1-phenyl-cis-1,2-cyclohexanediol (cis-PCD), has been studied under supersonic expansion conditions by combining laser spectroscopy with quantum chemistry calculations. The presence of the phenyl substituent induces conformational locking relative to cis-1,2-cyclohexanediol (cis-CD), and only one conformer of the bare molecule is observed by both Raman and IR-UV double resonance spectroscopy. The homochiral preference inferred for the dimer formation at low enough temperature is in line with the formation of a conglomerate in the solid state. The change in clustering propensity in cis-PCD relative to trans-1,2-cyclohexanediol (trans-CD), which shows heterochiral preference, is explained by the presence of the phenyl substituent rather than the effect of cis-trans isomerism. Indeed the transiently chiral cis-CD also forms preferentially heterodimers, whose structure is very close to that of the corresponding trans-CD dimer.

Vibrational Circular Dichroism Spectroscopy of Chiral Molecular Crystals: Insights from Theory

Chirality is a curious phenomenon that appears in various forms. While the concept of molecular (RS-)chirality is ubiquitous in chemistry, there are also more intricate forms of structural chirality. One of them is the enantiomorphism of crystals, especially molecular crystals, that describes the lack of mirror symmetry in the unit cell. Its relation to molecular chirality is not obvious, but still an open question, which can be addressed with chiroptical tools. Vibrational circular dichroism (VCD) denotes chiral infrared (IR) spectroscopy that is susceptible to both, the molecular as well as the intermolecular space by means of vibrational transitions. When carried out in the solid state, VCD delivers a very rich set of non-local contributions that are determined by crystal packing and collective motion. Since its discovery in the 1970s, VCD has become the method of choice for the determination of absolute configurations, but its applicability reaches beyond towards the study of different crystal forms and polymorphism. This brief review summarises the theoretical concepts of crystal chirality and how computations of solid-state VCD can shed light into the intimate connection of chiral structure and vibrational optical activity.

Conglomerate Crystallization in the Cambridge Structural Database (2020-2021)

Conglomerate crystals are materials capable of undergoing spontaneous resolution and were responsible for the discovery of molecular chirality. Their relevance to modern chemical and crystallographic sciences has been hindered by the difficulty in identifying and searching materials with this characteristic ability to spontaneously bias their own enantioenrichment. With the release of the November 2021 distribution of the Cambridge Structural Database (CSD) (version 5.43), a fresh quantity of chiral conglomerate crystals is expected to have been published in the CSD without identification. Indeed, no crystals in the CSD have been identified as a spontaneously resolving conglomerate crystal in their crystallographic information file since the 2019 release, despite the deposition of over 108,000 new crystal structures into the database over the same time period. A manual inspection of crystals deposited between 2020 and 2021 was conducted to identify 343 new chiral materials which exhibit conglomerate crystallization behavior. It is hoped that the continued manual curation of this list will aid those in the crystallographic and synthetic communities to study and exploit this spontaneous enantioenrichment behavior.

Enantioselectivity of chiral dihydromyricetin in multicomponent solid solutions regulated by subtle structural mutation

Multicomponent crystals of a chiral drug with non-chiral components have attracted increasing attention in the application of enantiomer purification and regulation of the physicochemical properties of crystalline materials. Crystalline solid solutions provide opportunities for fine-tuning material properties because of continuously adjustable component stoichiometry ratios. The synthesis, crystal structure, thermodynamics and solid-state enantioselectivity of a series of multicomponent crystals of chiral dihydromyricetin (DMY) with caffeine (CAF) or theophylline (THE) were investigated and the results reveal how the subtle change of molecular structure of the coformer dictates the enantiomer selectivity in multicomponent cocrystals. A series of multicomponent cocrystal solvates of chiral DMY with CAF and THE were synthesized by the slurry cocrystallization method in acetonitrile. Although most racemic mixtures crystallize as racemic compounds or conglomerates, both DMY-CAF and DMY-THE crystallize as chiral solid solutions, unveiled by pseudo-binary melt phase diagrams and pseudo-ternary solution phase diagrams. Crystal structures of Rac-DMY-CAF, R,R-DMY-CAF, Rac-DMY-THE and R,R-DMY-THE are reported for the first time via single-crystal X-ray diffraction, displaying two distinct types of solid solution differing in mixing scale of enantiomers spanning several orders of magnitude. Surprisingly, this remarkable impact on enantiomer discrimination was simply achieved by the reduction of a methyl group of CAF to the THE coformer, which was further rationalized from their crystal structures and intermolecular interactions. Collectively, this work has demonstrated that a subtle change in the molecular structure of a coformer can regulate enantioselectivity in crystalline materials, guiding the purification of chiral racemic compounds via the cocrystallization method and the design of solid-solution crystalline materials.

How Crystal Symmetry Dictates Non-Local Vibrational Circular Dichroism in the Solid State

Solid-State Vibrational Circular Dichroism (VCD) can be used to determine the absolute structure of chiral crystals, but its interpretation remains a challenge in modern spectroscopy. In this work, we investigate the effect of a twofold screw axis on the solid-state VCD spectrum in a combined experimental and theoretical analysis of P2₁ crystals of (S)-(+)-1-indanol. Even though the space group is achiral, a single proper symmetry operation has an important impact on the VCD spectrum, which reflects the supramolecular chirality of the crystal. Distinguishing between contributions originating from molecular chirality and from chiral crystal packing, we find that while IR absorption hardly depends on the symmetry of the space group, the situation is different for VCD, where completely new non-local patterns emerge. Understanding the two underlying mechanisms, namely gauge transport and direct coupling, will help to use VCD to distinguish polymorphic forms.

Identifying a Hidden Conglomerate Chiral Pool in the CSD

Conglomerate crystallization is the spontaneous generation of individually enantioenriched crystals from a nonenantioenriched material. This behavior is responsible for spontaneous resolution and the discovery of molecular chirality by Pasteur. The phenomenon of conglomerate crystallization of chiral organic molecules has been left largely undocumented, with no actively curated list available in the literature. While other crystallographic behaviors can be interrogated by automated searching, conglomerate crystallizations are not identified within the Cambridge Structural Database (CSD) and are therefore not accessible by conventional automated searching. By conducting a manual search of the CSD and literature, a list of over 1800 chiral species capable of conglomerate crystallization was curated by inspection of the racemic synthetic routes described in each publication. The majority of chiral conglomerate crystals are produced and published by synthetic chemists who seldom note and rarely exploit the implications this phenomenon can have on the enantiopurity of their crystalline materials. With their structures revealed, we propose that this list of compounds represents a new chiral pool which is not tied to biological sources of chirality.

Unbalanced racemates: solid state solutions containing enantiomeric pairs crystallizing in Sohncke space groups with (L:D) ratios other than (1:1) – illustrated with crystals of a Co(III) coordination compound

Herein we describe materials of composition [Co(NH3)4(X-leucinato)]I2·H2O in which the amino acid ligand is either L or D, and in which (a) while in pure enantiomorphic form (L), crystallizes in a Sohncke space group with Z′ = 2.0; but, whose packing closely resembles that of its racemate. Such substances are labeled a Racemic Mimic; and (b) crystals in which the L:D ratio of the amino acid ligand in the asymmetric unit is (71:29), which interestingly crystallize in the same space group and cell constants as those of the former. Moreover, the packing behavior is essentially the same in both—the difference being that the (1:1) species is fully ordered, while that with L:D (71:29) ratio has a partially disordered propyl chain. The (71:29) species we describe herein as an Unbalanced Racemate.

Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers

It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.

Pervasive approximate periodic symmetry in organic P1 structures

The goal of this project was to identify the prevalence of approximate symmetry in organic P1 structures. In the November 2019 version of the Cambridge Structural Database (CSD), there are 2592 organic, P1, R ≤ 0.050 structures; complete, unique entries are available for 1407 Z = Z' > 1 and 1049 Z = Z' = 1 structures. All the Z > 1 structures can have approximate symmetry; the Z = 1 structures were scanned to find those composed of molecules or ions that might lie on a special position and those that have two or more large molecules or ions that are very similar. The number of Z = 1 structures so identified was 285, of which 49 were grouped with the Z > 1 structures because Z_effective > 1. The packing in each of the 1407 + 285 = 1692 structures was investigated. The 144 that should almost certainly have been described in a smaller or higher-symmetry unit cell were removed from the list; 120 of the 144 are composed of achiral or racemic material. (About half of the Z = 1 and 89% of the Z > 1 structures are composed of enantiopure material.) Approximate periodic symmetry was found in 86% of the 1337 remaining Z > 1 structures and in 72% of the 211 remaining Z = 1 structures. About a third of the enantiomerically pure structures mimic inversion symmetry; 38% have approximate rotational symmetry. For the structures of achiral and racemic material, distorted glide or mirror symmetry is more common than is distorted inversion symmetry. Approximate rotational and glide symmetry was found to be periodic in two dimensions considerably more often than in three. In 4% of the structures, different layer types alternate or layers are related by approximate local rotations, as well as by small translations. In 5% of the structures, different parts of the molecule are segregated into two-dimensional regions that have different approximate symmetries. More than a third of the structures that are a distorted version of a higher-symmetry structure were determined at T ≥ 288 K.

Phosphorus-Nitrogen Compounds. Part 65. Novel diansa-spiro-cyclotetraphosphazenes: synthesis, characterization, bioactivity and electrochemical properties, fabrication of dye-sensitized solar cell studies

In this investigation, the substitution reaction of octachlorocyclotetraphosphazene, N4P4Cl8 (tetramer, OCCP, 1) with sodium 3-(N-ferrocenylmethylamino)-1-propanoxide (L1) was found to yield the compounds, 2,4-ansa- (2) and spiro- (2) cyclotetraphosphazene derivatives. The...

Ring D-Modified and Highly Reduced Angucyclinones From Marine Sediment-Derived Streptomyces sp

Angucyclines and angucyclinones represent the largest family of type II PKS-engineered natural products. Chemical analysis of a marine Streptomyces sp. KCB-132 yielded three new members, actetrophenone A (1) and actetrophenols A–B (2–3). Their structures were elucidated by NMR spectroscopy, X-ray crystallography and CD calculations. Actetrophenone A (1) is the first representative of a novel-type angucyclinone bearing a nonaromatic D-ring. Actetrophenol A (2) features a highly reduced and aromatized four-ring system, which is unprecedented for natural products. While (R_a)- and (S_a)-actetrophenol B (3) bear an unprecedented N-acetyltryptamine-substituted tetraphene core skeleton, this is the first report of a pair of atropisomeric isomers in the angucyclinone family. Actetrophenol A (2) exhibits remarkable antibiotic activity, notably including potent activity to multiple resistant Staphylococcus aureus and Enterococcus faecium with MIC values of 4 μg/ml, in contrast, the positive control antimicrobial agent penicillin was inactive up to 32 μg/ml.

Symmetry and chirality in crystals

A classification scheme relating the chirality of molecules to the type of crystal structures (chiral or achiral) they may form is presented. With respect to similar classifications proposed in the past, some corrections and extensions are introduced. In particular, (1) it is shown that chiral crystal structures from achiral molecules can occur in 28 types of space group having screw axes np , with p ≠ n/2, not in any Sohncke type of space group; (2) it is shown that the restriction on Z′ > 1 for kryptoracemates is contradicted by examples with Z′ = 1; and (3) the case of scalemic enantioenriched solutions, absent from most classifications, is included. Chiral crystal structures from purely inorganic (non-molecular) compounds are addressed too.

Approximate symmetry in the third reported structure of a metal complex of L-DOPA

Although l -DOPA is a major drug that has been used for more than 50 years to treat the motor symptoms of Parkinson’s disease, the Cambridge Structural Database contains only two structures in which it is coordinated to a metal. Why are there not more? The new structure is also notable for an approximate 42 axis.

Amino acid hydrogen oxalate quasiracemates – sulfur containing side chains

A new family of quasiracemic materials constructed from sulfur-containing amino acid hydrogen oxalates form supramolecular assemblies that divert significantly from near centrosymmetric alignment.

Spontaneous and Controlled Macroscopic Chiral Symmetry Breaking by Means of Crystallization

In this paper, macroscopic chiral symmetry breaking refers to as the process in which a mixture of enantiomers departs from 50–50 symmetry to favor one chirality, resulting in either a scalemic mixture or a pure enantiomer. In this domain, crystallization offers various possibilities, from the classical Viedma ripening or Temperature Cycle-Induced Deracemization to the famous Kondepudi experiment and then to so-called Preferential Enrichment. These processes, together with some variants, will be depicted in terms of thermodynamic pathways, departure from equilibrium and operating conditions. Influential parameters on the final state will be reviewed as well as the impact of kinetics of the R ⇔ S equilibrium in solution on chiral symmetry breaking. How one can control the outcome of symmetry breaking is examined. Several open questions are detailed and different interpretations are discussed.

Structural Elucidation of Enantiopure and Racemic 2-Bromo-3-Methylbutyric Acid

Halogenated carboxylic acids have been important compounds in chemical synthesis and indispensable research tools in biochemical studies for decades. Nevertheless, the number of structurally characterized simple α-brominated monocarboxylic acids is still limited. We herein report the crystallization and structural elucidation of (R)- and rac-2-bromo-3-methylbutyric acid (2-bromo-3-methylbutanoic acid, 1) to shed light on intermolecular interactions, in particular hydrogen bonding motifs, packing modes and preferred conformations in the solid-state. The crystal structures of (R)- and rac-1 are revealed by X-ray crystallography. Both compounds crystallize in the triclinic crystal system with Z = 2; (R)-1 exhibits two crystallographically distinct molecules. In the crystal, (R)-1 forms homochiral O–H···O hydrogen-bonded carboxylic acid dimers with approximate non-crystallographic C2 symmetry. In contrast, rac-1 features centrosymmetric heterochiral dimers with the same carboxy syn···syn homosynthon. The crystal packing of centrosymmetric rac-1 is denser than that of its enantiopure counterpart (R)-1. The molecules in both crystal structures adopt a virtually identical staggered conformation, despite different crystal environments, which indicates a preferred molecular structure of 1. Intermolecular interactions apart from classical O–H···O hydrogen bonds do not appear to have a crucial bearing on the solid-state structures of (R)- and rac-1.

Kryptoracemic compound hunting and frequency in the Cambridge Structural Database

Determination of kryptoracemic compound frequency in the Cambridge Structural Database using CCDC Python API script.

Chirality and stereoisomerism of organic multicomponent crystals in the CSD

Multicomponent crystals in the CSD are classified into 49 subclasses based on chirality and residue type.