To Avoid Chasing Incorrect Chemical Structures of Chiral Compounds: Raman Optical Activity and Vibrational Circular Dichroism Spectroscopies

Synthesis, characterization and absolute configurations of methyl ladderanoates

Methyl esters of [5]-ladderanoic acid and [3]-ladderanoic acid were prepared by esterification of the acids isolated from biomass at a wastewater treatment plant. Optical rotations at six different wavelengths (633, 589, 546, 436, 405 and 365 nm) and vibrational circular dichroism (VCD) spectra in the 1800-900 cm^-1 region were measured in CDCl₃ solvent and compared with quantum chemical (QC) predictions using B3LYP functional and 6-311++G(2d,2p) basis set with polarizing continuum model representing the solvent. QC predictions gave negative optical rotations at all six wavelengths for (R)-methyl [5]-ladderanoate and positive optical rotations for (R)-methyl [3]-ladderanoate, the same signs as previously reported for the corresponding acids. The crystal structure of (-)-methyl [5]-ladderanoate independently confirmed (R) configuration. The QC-predicted VCD spectra using Boltzmann population weighted spectra of individual conformers did not provide satisfactory quantitative agreement with the experimental VCD spectra. An improved quantitative agreement for VCD spectra could be obtained when conformer populations were optimized to maximize the similarity between experimental and predicted VCD spectra, but more improvements in VCD predictions are needed.

Chiral Molecular Structure Determination for a Desired Compound Just from Its Molecular Formula and Vibrational Optical Activity Spectra

A novel proof-of-concept model for chiral molecular structure determination using just the molecular formula and vibrational optical activity (VOA) spectra is presented. To verify this concept, the molecular formula of a desired compound is used to generate all possible chiral structural isomers and their VOA spectra are predicted. The similarity analyses of predicted VOA spectra were then carried out in two different ways: (a) similarity between VOA spectrum of one structural isomer with those of the rest, referred to as cross-correlations; (b) similarity between VOA spectra of all chiral structural isomers with the experimental VOA spectra of the desired compound. Three different molecular formulae, C₄H₈O, C₃H₅ClO, and C₆H₁₀O, and their chiral structural isomers (6, 9, and 75 respectively), were investigated. In each case, the correct chiral molecular structure of the desired compound was identified without ambiguity. Cross-correlation analysis revealed the uniqueness of VOA spectra in deducing the chiral molecular structure solely from its molecular formula. Different chiral structural isomers associated with the molecular formula CH₃NO₂ were also found to have no significant cross-correlations between their VOA spectra, opening a pathway to detect and identify the elusive chiral N-hydroxyoxaziridine from its VOA spectra.

Absolute configuration of seco-eudesmanolide inuloxin D from experimental and predicted chiroptical studies of its 4-O-acetyl derivative

Sesquitepenoids inuloxins A-D, belonging to different subgroups, were isolated from Dittrichia viscosa and showed potential biocontrol of some parasitic plants as Pelipanche, Orobanche, and Cuscuta species. The absolute configurations of the first three inuloxins A-C were previously determined by using experimental and computational chiroptical spectroscopic methods. The absolute configuration of inuloxin D remains to be established. The bioactive inuloxin E, closely related to inuloxin D, was recently isolated from the same plant organic extract. The same relative configuration of inuloxin D was assigned to inuloxin E by comparison of their NMR spectroscopic data. The absolute configurations of inuloxin D and inuloxin E are suggested in this work by analysis of the experimental and predicted chiroptical properties of the 4-O-acetyl derivative of inuloxin D.

New Techniques of Structure Elucidation for Sesquiterpenes

The most significant new techniques that have been used in the twenty-first century for the structure elucidation of sesquiterpenes and some derivatives are reviewed in this chapter. A distinctive feature of these methodologies is the combination of accurate experimental measurements with theoretical data obtained by molecular modeling calculations that allow to visualize, understand, and quantify many structural characteristics. This has been the case for NMR spectroscopy, which has expanded its potential for solving complex structural problems by means of comparison with quantum mechanical molecular models. Ab initio and density functional theory calculations of chemical shifts, coupling constants, and residual chemical shift anisotropies have played important roles in the solution of many structures of sesquiterpenes. The assignments of their absolute configurations by evaluation of calculated and experimental chiroptical properties as electronic and vibrational circular dichroism are also reviewed. This chapter also includes the use of X-ray diffraction analysis with emphasis on calculations of the Flack and Hooft parameters, which are applicable to all molecules that crystallize in non-centrosymmetric space groups. The accurate molecular models of sesquiterpenes, validated by concordance with their experimental properties, are nowadays essential for the interpretation of the effects of these natural products on biological systems.

How important are the intermolecular hydrogen bonding interactions in methanol solvent for interpreting the chiroptical properties?

Two crispine A analogs and tetrahydrofuro[2,3-b]furan-3,3a(6aH)-diol, endowed with hydroxyl groups that can participate in intramolecular hydrogen bonding, have been synthesized and experimental vibrational circular dichroism (VCD) spectra and optical rotatory dispersion (ORD) data have been measured in CD₃OD/CH₃OH solvents. The absolute configurations (ACs) of these compounds have been determined using their synthetic schemes, supplemented wherever possible with X-ray diffraction data. The ACs are also analyzed with quantum chemical (QC) calculations of VCD and ORD utilizing implicit solvation as well as explicit solvation models, with the later employing classical molecular dynamics (MD) simulations. It is found that VCD calculations with implicit solvation model are adequate for determining the ACs, despite propensity of studied compounds for intermolecular hydrogen bonding between solute and solvent molecules. This observation is important because time-consuming MD simulations may not be necessary in the type of situations studied here. Additionally, it is found that the QC predicted VCD spectra provided enough diastereomer discrimination for determining the correct AC of studied compounds independently. The same observation did not apply to ORD.

Basis set dependence of S[double bond, length as m-dash]O stretching frequencies and its consequences for IR and VCD spectra predictions

Benchmarking functionals and basis sets for the computational prediction of molecular properties is usually done on very small model systems. Larger organic molecules containing heavier second row atoms are not the typical model structures. We herein present the first survey of basis sets and functionals for the prediction of the IR and VCD spectra of chiral tosylates and sulfinates as we noted drastic deviations between computed harmonic frequencies obtained at B3LYP/6-311++G(2d,p) level of theory and those observed in experimental solution phase IR and VCD spectra. We show that the harmonic frequencies of the asymmetric and symmetric S[double bond, length as m-dash]O stretching modes of tosylates are predicted at significantly too low vibrational frequencies if the employed basis set does not provide higher order polarization functions. The results of our benchmarks show that at least the 6-311G(3df,2dp) basis (or equivalent Dunning and Ahlrichs variants) should be used.

Enhancement of the chiroptical response of α-amino acids via N-substitution for molecular structure determination using vibrational circular dichroism

The chiroptical response in the form of vibrational circular dichroism (VCD) in the midinfrared region is found to be enhanced when a hydrogen of amino group of l-tryptophan is substituted with acetyl, acryloyl, or maleyl group. The order of preference for VCD enhancement is found to be acryloyl > acetyl > maleyl group. The resulting experimental VCD spectra are also found to be satisfactorily reproduced by the quantum mechanical (QM) predicted spectra. The QM predicted spectra were simulated using the conformer populations, (a) predicted by Gibbs energies and (b) optimized to maximize the similarity between experimental and predicted VCD spectra. It is found that the conformer populations predicted by Gibbs energies do not yield the maximum possible similarity between experimental and the QM predicted spectra. This work identifies the N-substitution of α-amino acids and determining the conformer populations that best reproduce the experimental spectra as two new approaches for molecular structure determination.

Luminescent and Chiroptical Properties of 1 : 1 Eu (III) : Tetracycline Species Probed by Circularly Polarized Luminescence

This study investigates the significantly different luminescent and chiroptical properties of tetracycline (TC) when coordinated to Eu(III). The approach involves understanding the 1) speciation of TC and 2) conformation and species formed between Eu(III) and TC in a ratio of 1 : 1 in a dimethylformamide (DMF) solution and as a function of the pH value. By identifying the conformational changes of the various 1 : 1 Eu(III) : TC species, the results from this study explain information on the local microenvironment about the Eu(III) metal center. In particular, ⁵ D₀ ←⁷ F₀ Eu(III) laser excitation spectroscopy was employed to distinguish the different types of species found in solution in order to understand the interaction between Eu(III) and TC. On the other hand, circularly polarized luminescence (CPL) spectroscopy was used to understand the structural changes within the 1 : 1 Eu(III) : TC complex that could be related to the chirality of the Eu(III)-containing species. The CPL spectrum serves as a "fingerprint" to indicate the conformational changes within the 1 : 1 Eu(III) : TC complex as a result of the chiroptical signal arising from the various Eu(III) : TC species.

Vibrational optical activity for structural characterization of natural products

This review presents the recent progress towards elucidating the structures of chiral natural products and applications using vibrational optical activity (VOA) spectroscopy.

Absolute Configurations of Synthetic Molecular Scaffolds from Vibrational CD Spectroscopy

Vibrational circular dichroism (VCD) spectroscopy is one of the most powerful techniques for the determination of absolute configurations (AC), as it does not require any specific UV/vis chromophores, no chemical derivatization, and no growth of suitable crystals. In the past decade, it has become increasingly recognized by chemists from various fields of synthetic chemistry such as total synthesis and drug discovery as well as from developers of asymmetric catalysts. This perspective article gives an overview about the most important experimental aspects of a VCD-based AC determination and explains the theoretical analysis. The comparison of experimental and computational spectra that leads to the final conclusion about the AC of the target molecules is described. In addition, the review summarizes unique VCD studies carried out in the period 2008-2018 that focus on the determination of unknown ACs of new compounds, which were obtained in its enantiopure form either through direct asymmetric synthesis or chiral chromatography.

Dissymmetry Factor Spectral Analysis Can Provide Useful Diastereomer Discrimination: Chiral Molecular Structure of an Analogue of (-)-Crispine A

(1R,10bR)-1'-((R)-1,2-Dihydroxyethyl)-1-hydroxy-8,9-dimethoxy1,5,6,10b-tetrahydropyrrolo [2,1-a]isoquinolin-3(2H)-one, an analogue of (-)-crispine A, with three stereogenic centers is synthesized and its absolute configuration (AC) established using the combined information derived from the synthetic scheme and single crystal X-ray diffraction data. The experimental chiroptical spectra (namely, optical rotatory dispersion (ORD), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD)) and the corresponding quantum chemical (QC) predicted spectra for all diastereomers are used to evaluate the AC. The AC of the synthesized compound could be correctly established using any one of the three chiroptical spectroscopic methods (ORD, ECD, or VCD) when the relative configuration is constrained to be that derived from X-ray data or when the ACs of two of the chiral centers are constrained to be those derived from the synthetic scheme. In the absence of this outside information, the QC predicted ORD, ECD, and VCD for incorrect diastereomers are also found to satisfactorily reproduce the corresponding experimental spectra. Nevertheless, incorrect diastereomers could be eliminated when combined electronic dissymmetry factor (EDF) and vibrational dissymmetry factor (VDF) spectral analyses are included, leaving the correct diastereomer as the sole choice. Thus, the combined EDF and VDF spectral analysis is seen to be a helpful diastereomer discrimination tool.

Chiral Molecular Structures of Substituted Indans: Ring Puckering, Rotatable Substituents, and Vibrational Circular Dichroism

The chiral molecular structures of four different substituted indans, namely, (S)-1-methylindan, (R)-1-methylindan-1-d, (R)-1-aminoindan, and (S)-1-indanol, were investigated using experimental vibrational absorption and vibrational circular dichroism spectra and corresponding spectra predicted using quantum chemical (QC) calculations. All of these molecules possess two ring puckering conformations, with ring puckering leading to the pseudoequatorial substituent being approximately four times more abundant over that leading to the pseudoaxial substituent. The amino group in 1-aminoindan has three conformations arising from the rotation of NH₂ group, for each ring puckering conformation, resulting in a total of six conformations. Whereas 1-indanol in the nonhydrogen-bonding solvent CCl₄ also has six conformations similar to those of 1-aminoindan, 1-indanol in the hydrogen-bonding solvent DMSO-d ₆ adopts numerous conformations, of which 30 conformers are considered to have at least ∼1% or more population. In DMSO solution, ring puckering leading to pseudoequatorial substituent accounts for 77% population and 23% for pseudoaxial substituent. The QC spectra predicted for the geometry optimized conformers are found to be in excellent quantitative agreement with corresponding experimental spectra in all of the molecules considered. The procedures suggested in this work are hoped to provide successful pathways for future chiral molecular structural analyses.

Applications of OR/ECD/VCD to the structure elucidation of natural products

OR, ECD and VCD are powerful methods to determine the absolute configuration of natural products either applied independently or in combination.