Enhanced Structure-Based Prediction of Chiral Stationary Phases for Chromatographic Enantioseparation from 3D Molecular Conformations.

The accurate prediction of suitable chiral stationary phases (CSPs) for resolving the enantiomers of a given compound poses a significant challenge in chiral chromatography. Previous attempts at developing machine learning models for structure-based CSP prediction have primarily relied on 1D SMILES strings [the simplified molecular-input line-entry system (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings] or 2D graphical representations of molecular structures and have met with only limited success. In this study, we apply the recently developed 3D molecular conformation representation learning algorithm, which uses rapid conformational analysis and point clouds of atom positions in the 3D space, enabling efficient chemical structure-based machine learning. By harnessing the power of the rapid 3D molecular representation learning and a data set comprising over 300,000 chromatographic enantioseparation records sourced from the literature, our models afford notable improvements for the chemical structure-based choice of appropriate CSP for enantioseparation, paving the way for more efficient and informed decision-making in the field of chiral chromatography.

New mathematical measures for apprehending complexity of chiral molecules using information entropy.

In this paper, we present several new theoretical measures based on information entropy that can be used to analyze the information content of a chiral molecule. Starting from a differentiation between "chiral" and "achiral" portions in a chiral molecule, we define a new concept that allows us to quantify the complexity of chiral constitutional 2D-isomers of C10 to C20 alkanes. Various new chiral and achiral information measures founded on joint entropy, mutual information, and conditional entropy are presented providing an access to a set of regression equations. Then, introducing a case-based measure of entropy, we demonstrate that the distribution of the chiral complexity in these molecules is mostly skewed-right: 60% of the chiral isomers follow a 60/40 distribution rule, which indicates a concentration of chiral complexity in a small number of topological features. Furthermore, by replacing 2D topological distances by 3D distances, the application of these new information measures goes from conformational to racemization and deracemization studies. Interestingly, when the geometrical distances between atoms and the chiral center(s) are taken into account when determining the chiral information entropy, one can observe a significative Pearson correlation coefficient (R = 0.70) between the chiral entropy of 3D molecules and the continuous chirality measure. Finally, we show that our approach is applicable to almost any type of chiral organic chemical structures if in the entropy equation, atoms are represented by their electrotopological state (E-state) index instead of connectivity.

Atropisomerism in a 10-Membered Ring with Multiple Chirality Axes: (3 Z,9 Z)-1,2,5,8-Dithiadiazecine-6,7(5 H,8 H)-dione Series.

For the first time, chirality in (3 Z,9 Z)-1,2,5,8-dithiadiazecine-6,7(5 H,8 H)-dione series was recognized. Enantiomers of the 4,9-dimethyl-5,8-diphenyl analogue were isolated at room temperature, and their thermal stability was determined. X-ray crystallography confirmed the occurrence of a pair of enantiomers in the crystal. Absolute configurations were assigned by comparing experimental and calculated vibrational/electronic circular dichroism spectra of isolated enantiomers. A distorted tesseract (four-dimensional hypercube) was used to visualize the calculated enantiomerization process, which requires the rotation around four chirality axes. Conformers of higher energy as well as several concurrent pathways of similar energies were revealed.

Modeling and predicting chiral stationary phase enantioselectivity: An efficient random forest classifier using an optimally balanced training dataset and an aggregation strategy.

Predicting whether a chiral column will be effective is a daily task for many analysts. Moreover, finding the best chiral column for separating a particular racemic compound is mostly a matter of trial and error that may take up to a week in some cases. In this study we have developed a novel prediction approach based on combining a random forest classifier and an optimized discretization method for dealing with enantioselectivity as a continuous variable. Using the optimization results, models were trained on data sets divided into four enantioselectivity classes. The best model performances were achieved by over-sampling the minority classes (α ≤ 1.10 and α ≥ 2.00), down-sampling the majority class (1.2 ≤ α < 2.0), and aggregating multicategory predictions into binary classifications. We tested our method on 41 chiral stationary phases using layered fingerprints as descriptors. Experimental results show that this learning methodology was successful in terms of average area under the Receiver Operating Characteristic curve, Kappa indices and F-measure for structure-based prediction of the enantioselective behavior of 34 chiral columns.

Mining Chromatographic Enantioseparation Data Using Matched Molecular Pair Analysis.

We apply matched molecular pair (MMP) analysis to data from ChirBase, which contains literature reports of chromatographic enantioseparations. For the 19 chiral stationary phases we examined, we were able to identify 289 sets of pairs where there is a statistically significant and consistent difference in enantioseparation due to a small chemical change. In many cases these changes highlight enantioselectivity differences between pairs or small families of closely related molecules that have for many years been used to probe the mechanisms of chromatographic chiral recognition; for example, the comparison of N-H vs. N-Me analytes to determine the criticality of an N-H hydrogen bond in chiral molecular recognition. In other cases, statistically significant MMPs surfaced by the analysis are less familiar or somewhat puzzling, sparking a need to generate and test hypotheses to more fully understand. Consequently, mining of appropriate datasets using MMP analysis provides an important new approach for studying and understanding the process of chromatographic enantioseparation.

A screening study of ChirBase molecular database to explore the expanded chiral pool derived from the application of chiral chromatography.

28,000 chiral compounds separated by chiral chromatography have been selected in ChirBase database. The enantiomers of this library can be considered as potentially being isolable by chromatography at a small-scale level of development. The resulting chiral pool was analysed with the aim to describe compound molecular diversity as well as druglike and lead-like characteristics. In parallel, we have explored the possibility of using this chiral product library as starting materials for the construction of a virtual chiral combinatorial library. The chemical space occupied by the obtained combinatorial collection of new chiral scaffolds revealed that structures of the chromatographic-based chiral library may also be a source of chiral diversity for drug discovery. Another interesting in silico approach consisted to release all the protected or derivatized compounds. This procedure allowed us to enrich and expand the existing library with several thousands of original small chiral amines, acids and alcohols. Finally, sub-similarity searching strategies were found valuable for quickly selecting suitable small chiral precursors that are readily available from chiral chromatography for the small-scale synthesis of some known chiral drugs.

Toward structure-based predictive tools for the selection of chiral stationary phases for the chromatographic separation of enantiomers.

ChirBase, a database for the chromatographic separation of enantiomers containing more than 200,000 records compiled from the literature, was used to develop quantitative structure activity models for the prediction of which chiral stationary phase will work for the separation of a given molecule. Constructuion of QSAR models for the enantioseparation of nineteen chiral stationary phases was attempted using only analyte structural information, leading to the producton of self-consistent models in four cases. These models were tested by predicting which in-house racemic compounds would and would not be resolved on the different columns. Some degree of success was observed, but the sparseness of data within ChirBase, which contains enantioseparations for only a subset of molecules on a subset of columns under a variety of conditions may limit the creation of effective models. Augmented data sets gleaned from automated chromatographic method development systems deployed in academic and industrial research laboratories or the use of models that take other factors such as solvent composition, temperature, etc. into account could potentially be useful for the development of more robust models.

Chiral liquid chromatography contribution to the determination of the absolute configuration of enantiomers.

The review covers examples in which chiral HPLC, as a source of pure enantiomers, has been combined with classical methods (X-ray, vibrational circular dichroism (VCD), enzymatic resolutions, nuclear magnetic resonance (NMR) techniques, optical rotation, circular dichroism (CD)) for the on- or off-line determination of absolute configuration of enantiomers. Furthermore, it is outlined that chiral HPLC, which associates enantioseparation process and classical purification process, opens new perspectives in the classical determination of absolute configuration by chemical correlation or chemical interconversion methods. The review also contains a discussion about the various approaches to predict the absolute configuration from the retention behavior of the enantiomers on chiral stationary phases (CSPs). Some examples illustrate the advantages and limitations of molecular modeling methods and the use of chiral recognition models. The assumptions underlying some of these methods are critically analyzed and some possible emerging new strategies are outlined.

Enantiomers of dimethyl [(2E)-1,3-diphenylprop-2-en-1-yl]propanedioate resulting from allylic alkylation reaction: elution order on major high-performance liquid chromatography chiral columns.

Asymmetric allylic alkylation leading to dimethyl [(2E)-1,3-diphenylprop-2-en-1-yl]propanedioate 1 is a privileged reaction which has been considered in more than 800 references from 1985 to early 2012. This paper thus begins with a thorough review of the literature with a particular focus on the way the ee's and absolute configuration of the prevailing enantiomer were claimed and reported by the authors. In a large majority of articles chiral chromatography is used for ee's determination. Unfortunately, in too many cases the data, the column or the eluent are not provided. In a significant proportion (5%) the column name is ambiguous. Furthermore, several discrepancies are detected in the assigned order of elution when chiral chromatography data are provided. We therefore decided to firmly establish the chromatographic behavior of the enantiomers of 1, which were obtained from the corresponding racemate by semi-preparative chiral chromatography and their absolute configuration assigned by ECD and VCD spectroscopies. ORD curves show that optical rotation is very weak at 350 nm with indication of inversion of the sign at lower wavelengths. It results in a low sensitivity for on line JASCO polarimeter detector. Chiroptical detection was nicely performed by on line JASCO CD detector set at 254 nm: (-)-(S)-1 shows a (+)-CD(254 nm) sign. Pure enantiomers of authenticated absolute configuration allowed a safe assignment of the order of elution during HPLC or SFC on major chiral stationary phases. Quite interestingly for practical application, the order of elution is reversed on Chiralpak AD-H and IA on going from hexane/EtOH to hexane/2-PrOH in HPLC or on going from CO(2)/EtOH (or MeOH) to CO(2)/2-PrOH in SFC.

Enantiophore modeling in 3D-QSAR. A data mining application on Whelk-O1 chiral stationary phase.

A combination of the enantiophore concept described in a previous study and a quantitative structure enantioselective relationship (QSER) based on partial least squares (PLS) analysis is presented. In the present study, a comprehensive approach for describing the enantioselective binding properties of the Whelk-O1 chiral HPLC receptor is achieved using molecular descriptors calculated by the GRID program. The GRID descriptors allow us to describe the molecules in terms of their ability to form favorable interactions with independent chemical groups (probes) that can be related to receptor sites. For each molecule, we compute 120 enantiophore descriptors representing the energy contributions from all possible pairwise combinations of probes. The overall procedure was simplified by considering only the most energetically favorable locations and converting selected grid-point energies into alignment-independent descriptors. By using a training set of 143 diverse chiral compounds, an optimal PLS model requiring seven components was chosen by using the cross-validation method resulting in a correlation coefficient R2= 0.88 and a cross validated correlation coefficient Q2= 0.85. An interpretation of the model is proposed based upon a visual inspection of the regression coefficient plots. From these plots, the influence of particular molecular features for selective binding of solutes was estimated and used to outline the chiral recognition sites in the Whelk-O1 receptor. The predictive power of our model has been estimated by means of an external data set emphasizing the suitability of the procedure also for predictive aims.

Data mining and enantiophore studies on chiral stationary phases used in HPLC separation.

ChirBase database has been employed to mine the chemical structures of compounds resolved on common commercial chiral stationary phases (CSP). Different data sets were produced. The molecular fingerprint (enantiophore) strategy was then applied over these data sets. Enantiophores are identified by analyzing and mapping the three-dimensional common structural features shared by the ligand molecules imported from ChirBase. Such lists of encoded ligand enantiophores allowed us to generate 3D maps of the molecular interacting fragments, which are supposed to act reciprocally with each CSP. Results show that each CSP is combined with different preferential enantiophore counterparts in the ligand. These differences may be well related to the particular behavior of a given CSP to separate different families of compounds. As expected, supramolecular cellulosic or amylosic CSPs show generalist behavior by resolving a wide range of racemates. On the other hand, molecular CSPs based on a well-defined chiral receptor (such as Whelk-O1 or Chirobiotic T) appear to be more specific and thus specially adapted for more restrictive families of compounds. In addition, enantiophore analyses confirm that the supramolecular CSPs can combine multiple potential binding sites and so offer numerous enantioselective mechanisms toward a ligand. Inversely, on molecular CSPs, the ligand must respect strict geometrical constraints to make possible the chiral discrimination. Additional applications of the methodology are discussed as well.

Theoretical reassessment of Whelk-O1 as an enantioselective receptor for 1-(4-halogeno-phenyl)-1-ethylamine derivatives.

A combination of molecular mechanics and first principles calculations was used to explore the enantioselectivity of receptors, taking into account experimental data from the CHIRBASE database. Interactions between the Whelk-O1 HPLC chiral stationary phase with the complete series of 1-(4-halogeno-phenyl)-1-ethylamine derivative racemates were studied. The objective was to extract information from the interactions between the chiral Whelk-O1 stationary phase and the enantiomers, hence probing the origin of the enantioselective behavior. Calculations correctly reproduce the elution orders and reasonably describe the experimental enantioselectivities and retention factors. Different binding modes were observed for the first eluted enantiomer complexes, whereas the second eluted show only one prevalent diastereomeric binding fashion. Natural bond orbital (NBO) analysis was used on the global minima bound-complexes to quantify donor-acceptor interactions among chiral stationary phase and ligand moieties. Intermolecular hydrogen bonding was found to be the essential energetic interaction for all systems studied. CH-pi, aromatic stacking and various charge transfer interactions were found to be smaller in magnitude but still important for the global enantioselective behavior. The three-point interaction model is discussed, pointing out the difficulty of its application for the qualitative prediction of elution orders (absolute configurations).