A Holistic Approach to Determining Stereochemistry of Potential Pharmaceuticals by Circular Dichroism with ß-Lactams as Test Cases.

This paper's main objective is to show that many different factors must be considered when solving stereochemical problems to avoid misleading conclusions and obtain conclusive results from the analysis of spectroscopic properties. Particularly in determining the absolute configuration, the use of chiroptical methods is crucial, especially when other techniques, including X-ray crystallography, fail, are not applicable, or give inconclusive results. Based on various ß-lactam derivatives as models, we show how to reliably determine their absolute configuration (AC) and preferred conformation from circular dichroism (CD) spectra. Comprehensive CD analysis, employing both approaches, i.e., traditional with their sector and helicity rules, and state-of-the-art supported by quantum chemistry (QC) calculations along with solvation models for both electronic (ECD) and vibrational (VCD) circular dichroism ranges, allows confident defining stereochemistry of the ß-lactams studied. Based on an in-depth analysis of the results, we have shown that choosing a proper chiroptical method/s strictly depends on the specific case and certain structural features.

A Critical Appraisal of Dimolybdenum Tetraacetate Application in Stereochemical Studies of vic-Diols by Circular Dichroism.

This critical appraisal is intended for users of the dimolybdenum method, well-established in electronic circular dichroism (ECD) to determine the absolute configuration of vic-diols and, in particular, for experimental researchers not being experts in chiroptical methods. The main goal is to demonstrate how to avoid misleading and ambiguous conclusions resulting from the rigorous application of the helicity rule by limiting the analysis to the vic-diol unit alone. We particularly focused on multichromophoric systems, especially those that may interfere with the absorption of an in situ formed dimolybdenum tetraacetate-diol complex. In this context, examples are presented of vic-diols for which stereochemical assignment based solely on the helicity rule is ambiguous and does not necessarily lead to correct results. The motivation for choosing these examples was to demonstrate the impact of the structure of the substrate on the complexation process with the metal core and its selectivity. For each selected case, results obtained are analyzed in detail together with a discussion of existing restrictions and choice of a support method to increase the credibility of the conclusion. Based on seven both educational and challenging examples, it was shown that the dimolybdenum methodology can also be effectively applied to complex chromophoric systems, provided that other chiroptical methods and/or computational support verify obtained results.

Research into the oxidation of abietic acid-derived enone with atmospheric oxygen.

This work presents results of methyl 7-oxoabiet-13(14)-en-18-oate (3) self-oxidation with air-oxygen in the presence of various bases such as triethylamine or sodium t-butoxide. While under aerobic conditions, the use of sodium t-butoxide as a base results in the formation of four isomeric alcohols, an addition of triethylamine into reaction medium directs the enone 3 oxidation to hydroperoxides. To clarify this base dependence and to obtain more in-depth information about this reaction additional studies with cyclohexenone as a reference enone have been undertaken. Their results demonstrated the predisposition of abietane hydroperoxides to oxidize α,ß-unsaturated ketones to epoxides in the presence of t-butoxide while reducing the hydroperoxide group to hydroxyl. This ability of hydroperoxides to epoxidize conjugated double bonds and confirmed by the present study intermolecular course allowed proposing a plausible mechanism for this reaction.

Solvation of 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol revealed by circular dichroism: a case of chromane helicity rule breaking.

The primary goal of this work is to clarify why 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol {(S)-TMChM} deviates from the chromane helicity rule under solvent change. The rule, applicable to determining the absolute configuration of molecules containing the chromane chromophore, binds the sign of the 1Lb Cotton effect (CE) with the helicity of the dihydropyran ring. In case of TMChM, however, this CE exhibits extreme solvent dependence: it is negative in non-coordinating solvents and positive in coordinating ones, irrespective of the helicity of the heterocyclic ring. TD-DFT calculations using PCM and hybrid solvation models were performed to explain origin of this phenomenon. It turned out that the 1Lb CE sign directly depends on the position of the phenolic OH group at carbon atom C6 (OHC6). In the absence of interactions with solvents (as in CCl4 or nC6H14) or when a solvent plays proton donor role (as in CHCl3), the OHC6 lies in the phenyl plane and the 1Lb CE sign follows the P/M helicity rule. In contrast, in proton acceptor solvents, like DMSO, CH3OH or CH3CN, the OHC6 group is deflected from the phenyl plane, and the 1Lb CE sign of individual (S)-TMChM conformers depends on the sector in which the OHC6 is located. Thus, in solution, the 1Lb CE sign is an average over different orientations of the OHC6 group and can be positive (as in DMSO and CH3OH) or negative (as in CH3CN) which means that it does not follow the chromane helicity rule. The impact of OHC6 on the 1Lb CE sign and thus the conclusions for the stereochemistry of chromans are demonstrated here for the first time. Additionally, a comparison of experimental and simulated ECD spectra, supported by VCD data, allowed to determine the geometry of intermolecular clusters formed in different solvents.

In Depth Analysis of Chiroptical Properties of Enones Derived from Abietic Acid.

With the use of inexpensive commercially available abietic acid, a whole series of abietane enones were prepared in high yields. The structures of all the products obtained were determined by comprehensive spectroscopic analysis with particular emphasis on the use of advanced NMR techniques, comparison with previously reported data and, where possible, by single crystal X-ray diffraction. However, in cases where X-ray crystallography was not applicable or compounds tested were unstable, a final stereochemical assignment could be inferred only by electronic circular dichroism (ECD) supported by vibrational circular dichroism to increase credibility. To reveal the relationship between structure and chiroptical properties, we used combined experimental and theoretical analysis of geometries, structural parameters, and chiroptical properties of all enones synthesized. A thorough analysis of their conformational flexibility by examining the effect of solvent and temperature on the ECD spectra was also used to achieve desired objectives. As a result, the impact of substituents adjacent to the enone chromophore on the conformation was determined by demonstrating that even slight changes in the position of hydroxyl and isopropyl groups attached to carbon C13 may substantially affect ECD curves' pattern, leading in some cases to Cotton effects sign reversal.

Self-assembly of (boron-dipyrromethane)-diphenylalanine conjugates forming chiral supramolecular materials.

Herein, we present the synthesis of a series of boron-dipyrromethane (BDP) derivatives bearing diphenylalanine (FF) at their meso position via amide bond coupling. The BDP-FF bioconjugates are able to form self-assembled materials with different morphologies. By altering various parameters such as the protecting group of the FF peptide or the solvent system of the self-assembly process, we were able to obtain either fibrillar or spherical nanostructures. Furthermore, we confirmed that both the formation as well as the dissociation of the self-assemblies is a reversible procedure that can be achieved by simply altering the solvent mixture. Electronic circular dichroism (ECD) studies demonstrated a characteristic mirror image relationship regarding the FLFL and FDFD enantiomers, revealing the chiral nature of the obtained materials. Interestingly, an intense excitonic bisignate signal was observed in the ECD spectrum of the fibrillar structures, whereas the spherical assemblies remained ECD silent. What is more, the electronic circular dichroism studies were supported by quantum chemical calculations.

Circular dichroism spectroscopy and DFT calculations in determining absolute configuration and E/Z isomers of conjugated oximes.

The primary purpose of this work was to demonstrate the suitability of circular dichroism (CD) spectroscopy in stereochemical studies of α,ß-unsaturated oximes, with particular emphasis on determination of E and Z geometry of the oxime double bond. As models for this study, O-phenyl and O-triphenylmethyl (trityl) oximes of 4-hydroxy-2-methylcyclopent-2-en-1-one were selected. These model compounds differ in both absolute configuration at C4 carbon atom and E-Z configuration of the oxime double bond. The basic dichroic technique applied was electronic circular dichroism (ECD) assisted by quantum-chemical calculations and vibrational circular dichroism (VCD) for selected cases. Such an approach enabled effective implementation of both goals. Thus, we were able to associate the signs of Cotton effects in the range of 190-240 nm with the absolute configuration at C4 and within 240-300 nm with the E- or Z-geometry of the oxime double bond. Within this work, optical activity of the protecting trityl group was also studied towards formation of the propeller-shaped conformations by using the same combined CD/DFT methodology. As shown, the helical structure of the trityl group has a considerable influence on the ECD spectra. However, the MPM and PMP conformers of the trityl group are in fact almost equally populated in the conformational equilibrium, making it impossible to distinguish them. On the other hand, rotamers of the hydroxyl group at C4 show a decisive impact on the VCD spectra in both phenoxy and trityl oximes.

Chirality sensing of bioactive compounds with amino alcohol unit via circular dichroism.

The aim of the present work was to test various chiroptical techniques, including in particular the in situ dirhodium methodology, to assign the absolute configuration of 1,2- and 1,3-amino alcohols. As models, we selected mainly compounds that have both an additional strongly absorbing and interfering chromophoric system and application in medicinal chemistry. Determination of the absolute configuration (AC) of the tested molecules such as cinchona alkaloids, Tamiflu, and others was carried out using a combination of electronic and vibrational circular dichroism (ECD, VCD) spectroscopy. It has been demonstrated that both 1,2- and 1,3-aminol moieties are subject to the same sector rule correlating stereostructure of formed Rh2 -complex with chiroptical properties, and that the changes in the position of the stereogenic center do not affect its proper use.

Synthesis and comprehensive structural and physicochemical characterization of dutasteride hydrochloride hydrate solvates.

Four crystalline dutasteride hydrochloride hydrate solvates containing respectively methanol, ethanol, acetone and acetonitrile molecules were obtained. All samples were characterized by extensive spectroscopic analysis with infrared spectroscopy (FT-IR), differential scanning calorimetry (DSC) and 1H as well as 13C NMR techniques. For three solvates, i.e. methanol, ethanol and acetone solvates, the single crystal X-ray diffraction (SCXRD) experiments were possible, and their respective crystal and molecular structures were determined. The present study allowed to unambiguously establish the molecular composition of solvates as consisting of a dutasteride : hydrogen chloride : water : solvent in a molar ratio of 1:1:1:1 and confirm that they are isostructural. Beyond providing the full spectroscopic characteristic of the compounds, the results obtained have also allowed clarifying of some appearing inconsistencies in published literature regarding the appropriate attribution of IR absorption bands to the relevant molecular vibrations.

Denaturation of proteins by surfactants studied by the Taylor dispersion analysis.

We showed that the Taylor Dispersion Analysis (TDA) is a fast and easy to use method for the study of denaturation proteins. We applied TDA to study denaturation of ß-lactoglobulin, transferrin, and human insulin by anionic surfactant sodium dodecyl sulfate (SDS). A series of measurements at constant protein concentration (for transferrin was 1.9 x 10-5 M, for ß- lactoglobulin was 7.6 x 10-5 M, and for insulin was 1.2 x 10-4 M) and varying SDS concentrations were carried out in the phosphate-buffered saline (PBS). The structural changes were analyzed based on the diffusion coefficients of the complexes formed at various surfactant concentrations. The concentration of surfactant was varied in the range from 1.2 x 10-4 M to 8.7 x 10-2 M. We determined the minimum concentration of the surfactant necessary to change the native conformation of the proteins. The minimal concentration of SDS for ß-lactoglobulin and transferrin was 4.3 x 10-4 M and for insulin 2.3 x 10-4 M. To evaluate the TDA as a novel method for studying denaturation of proteins we also applied other methods i.e. electronic circular dichroism (ECD) and dynamic light scattering (DLS) to study the same phenomenon. The results obtained using these methods were in agreement with the results from TDA.

Design, synthesis and biological properties of seco-d-ring modified 1α,25-dihydroxyvitamin D3 analogues.

As a continuation of our efforts directed to the structure-activity relationship studies of vitamin D compounds, we present in this paper the synthesis of new analogues of 1α,25-(OH)2D3 characterized by numerous structural modifications, especially a cleaved D ring. Total synthesis of the CD fragment required for the construction of the target vitamins was based on the Stork approach. The structure of the key intermediate - bicyclic hydroxy lactone - was established by crystallographic and electronic circular dichroism (ECD) spectral analysis. Following the attachment of the hydroxyalkyl side chain, the formed D-seco Grundmann ketone was subjected to Wittig-Horner coupling with the corresponding A-ring phosphine oxides providing two desired D-seco analogues of 19-nor-1α,25-(OH)2D3, one without a substituent at C-2 and the other possessing a 2-exomethylene group. Both compounds were biologically tested and the latter was found to be more active in in vitro tests. Despite so many structural changes introduced in its structure, the biological activity of the 2-methylene analogue approached that of the natural hormone. The synthesized D-seco vitamins, however, proved to be inactive on bone and intestine in vivo.

Synthesis and Comprehensive Structural and Chiroptical Characterization of Enones Derived from (-)-α-Santonin by Experiment and Theory.

The aim of the present work is to explain the causes of the observed deviations from sector and helicity rules to determine the absolute configuration of optically active α,ß-unsaturated ketones by means of electronic circular dichroism (ECD). To this end, a series of model compounds with a common decahydronaphthalene skeleton representing both cisoid and transoid enones were synthesized. In the framework of this work, detailed dichroic studies supported by single crystal X-ray analysis were performed where possible. To assist the achievement of the desired objectives the conformational flexibility of the selected cis-enones through the dependence of solvent and temperature on the ECD spectra were examined. All experimental studies were supplemented by detailed DFT calculations. A notable result of the study is assessing the applicability of the enone sector and helicity rules in dichroic studies and potential restrictions. To this end, a number of factors that could determine the signs of the individual Cotton effects has been considered. Among these nonminimum structure effects, i.e., twisting of the enone chromophore and nonplanarity of the enone double bond can be mentioned.

Full Characterization of Linezolid and Its Synthetic Precursors by Solid-State Nuclear Magnetic Resonance Spectroscopy and Mass Spectrometry.

In this work, for the first time we report complementary structural and spectral studies of linezolid and its synthetic precursors (R)-N-{3-[3-fluoro-4-(morpholin-4-yl)phenyl]-2-oxooxazolidin-5-yl}methanol and (R)-N-{3-[3-fluoro-4-(morpholin-4-yl)phenyl]-2-oxooxazolidin-5-yl}methyl azide employing solid-state nuclear magnetic resonance (SS NMR) spectroscopy and electron ionization mass spectrometry. Each technique provides unique and specific set of information. Through high-resolution SS NMR using (13) C, (15) N, and (19) F as structural probes, we revealed dynamic molecular disorder in the crystal lattice for polymorphs II and III of linezolid, never reported before. Utilizing variable temperature (13) C cross-polarization magic-angle spinning technique, we proved that the disorder has a local character. Only morpholine residue of linezolid is under fast regime exchange at room temperature. This process slows down at a lower temperature and stopped at 213 K. The mass spectrometry revealed that chemical modification at oxazolidinone end of linezolid has a significant influence on fragmentation pathways of studied drug and its synthetic precursors. In particular, the compound that has azide group at the methyl substituent in the position C5 of the oxazolidinone ring is characterized by the most complicated fragmentation pattern, probably caused by thermal decomposition, which was taking place before ionization.

Prediction of ROA and ECD Related to Conformational Changes of Astaxanthin Enantiomers.

ECD, ROA, and VCD were used to characterize astaxanthin conformers that differ in their arrangements of the ß-ionone ring in respect to the chain. We obtained ECD spectra experimentally, and the ECD, ROA, and VCD spectra of both individual conformers and conformation-averaged mixtures were predicted using quantum-chemical calculations at the CAM-B3LYP level of theory using the PCM solvation model. The chiroptical methods employed (particularly ECD and ROA) were considerably more sensitive to conformational changes of astaxanthin compared to "mono-signed" conventional Raman spectroscopy. Strikingly, conformers that are the same optical isomers (e.g., of 3S,3'S-astxanthin), while geometrically nearly mirror images, exhibited sign-inversed ECD and ROA spectra. The conformational sensitivity of these chiroptical methods makes them a promising tool in the study of carotenoids in the natural environment (for instance, in de novo algal or yeast astaxanthin sources).

Comprehensive spectroscopic characterization of finasteride polymorphic forms. Does the form X exist?

The pure polymorphic forms I, II, and III of finasteride were prepared and their purity was confirmed by FTIR, differential scanning calorimetry, and X-ray powder diffraction measurements. The preparation experiments demonstrated that the desolvation process of some finasteride solvates does result not only in the formation of polymorphic forms I and II, but also in obtaining the pure form III. The (13)C cross-polarization magic angle spinning (CP-MAS) and the (15)N CP-MAS spectra can distinguish all three polymorphic forms of finasteride. Additionally, the data point to the presence of only one molecule in crystallographic asymmetric unit of polymorphic forms I and III and two molecules in the form II. The application of electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) spectroscopy for finasteride polymorphic forms shows that the three polymorphs could be distinguished by the characteristic shapes of their VCD spectra in the spectral range 1520-1440 cm(-1). The ECD spectral patterns of all these forms, however, are almost indistinguishable because of their close similarity. Comparison of the (13)C CP-MAS spectra of forms I, II, and III with those reported in the literature indicates that the so-called finasteride "form X" is identical to the previously known finasteride form III. On this basis, the existence of form X was excluded.

Synthesis of a sucrose dimer with enone tether; a study on its functionalization.

The reaction of appropriately functionalized sucrose phosphonate with sucrose aldehyde afforded a dimer composed of two sucrose units connected via their C6-positions ('the glucose ends'). The carbonyl group in this product (enone) was stereoselectively reduced with zinc borohydride and the double bond (after protection of the allylic alcohol formed after reduction) was oxidized with osmium tetroxide to a diol. Absolute configurations of the allylic alcohol as well as the diol were determined by circular dichroism (CD) spectroscopy using the in situ dimolybdenum methodology.

Amine-catalyzed direct aldol reactions of hydroxy- and dihydroxyacetone: biomimetic synthesis of carbohydrates.

This article presents comprehensive studies on the application of primary, secondary, and tertiary amines as efficient organocatalysts for the de novo synthesis of ketoses and deoxyketoses. Mimicking the actions of aldolase enzymes, the synthesis of selected carbohydrates was accomplished in aqueous media by using proline- and serine-based organocatalysts. The presented methodology also provides direct access to unnatural L-carbohydrates from the (S)-glyceraldehyde precursor. Determination of the absolute configuration of all obtained sugars was feasible using a methodology consisting of concerted ECD and VCD spectroscopy.

Chemoenzymatic approach to optically active 4-hydroxy-5-alkylcyclopent-2-en-1-one derivatives: an application of a combined circular dichroism spectroscopy and DFT calculations to assignment of absolute configuration.

A series of representative optically active derivatives of 4-hydroxy-5-alkylcyclopent-2-en-1-one were prepared from the respective 2-furyl methyl carbinols via the Piancatelli rearrangement followed by the enzymatic kinetic resolution of racemates. Applicability of chiroptical methods (experimental and calculated electronic circular dichroism [ECD] and vibrational circular dichroism [VCD] spectra) to determine the absolute configuration of both stereogenic centers in 4-hydroxy-5-methylcyclopent-2-en-1-one was demonstrated. It was also demonstrated that the concurrent application of ECD and VCD spectroscopy can be used for the determination of the configuration of two stereogenic centers.

Comprehensive chiroptical study of proline-containing diamide compounds.

The continuously growing interest in the understanding of peptide folding led to the conformational investigation of methylamides of N-acetyl-amino acids as diamide models. Here we report the results of detailed conformational analysis on Ac-Pro-NHMe and Ac-ß-HPro-NHMe diamides. These compounds were analyzed by experimental and computational methods, the conformational distributions obtained by Density Functional Theory (DFT) calculations for isolated and solvated diamide compounds are discussed. The conformational preference of proline-containing diamide compounds as a function of the ambience was observed by a number of chiroptical spectroscopic techniques, such as vibrational circular dichroism (VCD), electronic circular dichroism (ECD), Raman optical activity (ROA) spectroscopy, and additionally by single crystal X-ray diffraction analyses. Based on a comparison between Ac-Pro-NHMe and Ac-ß-HPro-NHMe, one can conclude that due to the greater conformational freedom of the ß-HPro derivative, Ac-ß-HPro-NHMe shows different behavior in solid- and solution-phase, as well. Ac-ß-HPro-NHMe tends to form cis Ac-ß-HPro amide conformation in water, dichloromethane, and acetonitrile in contrast to its α-Pro analog. On the other hand, the crystal structure of the ß-HPro compound cannot be related to any of the conformers obtained in vacuum and solution while the X-ray structure of Ac-Pro-NHMe was identified as tα(L)-, which is a trans Ac-Pro amide containing conformer also predominant in polar solvents.

Chromane helicity rule--scope and challenges based on an ECD study of various trolox derivatives.

The validity of the chromane helicity rule correlating the sense of twist within the dihydropyran ring with the CD sign of the (1)Lb band observed at ca. 290 nm in their electronic circular dichroism (ECD) spectra is examined using a set of natural (S)-trolox derivatives. To investigate both the scope and the limitations of the rule a combination of ECD spectroscopy, especially the temperature dependence of the ECD spectra, single crystal X-ray diffraction analyses, and density functional theory (DFT) calculations was used. A thorough conformational analysis supported by the X-ray data led to the identification of predominant conformers. Then, a comparison of the experimental ECD spectra with the spectra simulated by TDDFT calculations allowed for a reasonable interpretation of the accumulated data. The results clearly indicated that to avoid the possibility of erroneous conclusions the chromane helicity rule should be used with great caution. This is likely related to the conformational flexibility of tested compounds by which conformers of different helicities can be produced. Therefore, based on the results presented here, it is strongly recommended that the conclusions derived from analysis of experimental data are supported with the appropriate theoretical computations.