Conformational analysis of small organic molecules using NOE and RDC data: A discussion of strychnine and α-methylene-γ-butyrolactone

Influence of Solvent Polarity on the Conformer Ratio of Bicalutamide in Saturated Solutions: Insights from NOESY NMR Analysis and Quantum-Chemical Calculations

The study presents a thorough and detailed analysis of bicalutamide's structural and conformational properties. Quantum chemical calculations were employed to explore the conformational properties of the molecule, identifying significant energy differences between conformers. Analysis revealed that hydrogen bonds stabilise the conformers, with notable variations in torsion angles. Conformers were classified into 'closed' and 'open' types based on the relative orientation of the cyclic fragments. NOE spectroscopy in different solvents (CDCl3 and DMSO-d6) was used to study the conformational preferences of the molecule. NOESY experiments provided the predominance of 'closed' conformers in non-polar solvents and a significant presence of 'open' conformers in polar solvents. The proportions of open conformers were 22.7 ± 3.7% in CDCl3 and 59.8 ± 6.2% in DMSO-d6, while closed conformers accounted for 77.3 ± 3.7% and 40.2 ± 6.2%, respectively. This comprehensive study underscores the solvent environment's impact on its structural behaviour. The findings significantly contribute to a deeper understanding of conformational dynamics, stimulating further exploration in drug development.

Conformational Analysis of 1,5-Diaryl-3-Oxo-1,4-Pentadiene Derivatives: A Nuclear Overhauser Effect Spectroscopy Investigation

1,5-Diaryl-3-Oxo-1,4-Pentadiene derivatives are intriguing organic compounds with a unique structure featuring a pentadiene core, aryl groups, and a ketone group. This study investigates the influence of fluorine atoms on the conformational features of these derivatives in deuterated chloroform (CDCl3) solution. Through nuclear magnetic resonance (NMR) spectroscopy and quantum chemical calculations, we discerned variations in interatomic distances and established predominant conformer proportions. The findings suggest that the non-fluorinated entity exhibits a uniform distribution across various conformer groups. The introduction of a fluorine atom induces substantial alterations, resulting in the predominance of a specific conformer group. This structural insight may hold the key to their diverse anticancer activities, previously reported in the literature.

Ensemble determination by NMR data deconvolution

Nuclear magnetic resonance (NMR) is the spectroscopic technique of choice for determining molecular conformations in solution at atomic resolution. As solution NMR spectra are rich in structural and dynamic information, the way in which the data should be acquired and handled to deliver accurate ensembles is not trivial. This Review provides a guide to the NMR experiment selection and parametrization process, the generation of viable theoretical conformer pools and the deconvolution of time-averaged NMR data into a conformer ensemble that accurately represents a flexible molecule in solution. In addition to reviewing the key elements of solution ensemble determination of flexible mid-sized molecules, the feasibility and pitfalls of data deconvolution are discussed with a comparison of the performance of representative algorithms.

Structures Controlled by Entropy: The Flexibility of Strychnine as Example

To study the flexibility of strychnine, we performed molecular dynamics simulations with orientational tensorial constraints (MDOC). Tensorial constraints are derived from nuclear magnetic resonance (NMR) interaction tensors, for instance, from residual dipolar couplings (RDCs). Used as orientational constraints, they rotate the whole molecule and molecular parts with low rotational barriers. Since the NMR parameters are measured at ambient temperatures, orientational constraints generate conformers that populate the whole landscape of Gibbs free energy. In MDOC, structures are populated that are not only controlled by energy but by the entropy term TΔS of the Gibbs free energy. In the case of strychnine, it is shown that ring conformers are populated, which has not been discussed in former investigations. These conformer populations are not only in accordance with RDCs but fulfill nuclear Overhauser effect (NOE)-derived distance constraints and ³J_HH couplings as well.

Connection of Isolated Stereoclusters by Combining 13C-RCSA, RDC, and J-Based Configurational Analyses and Structural Revision of a Tetraprenyltoluquinol Chromane Meroterpenoid from Sargassum muticum

The seaweed Sargassum muticum, collected on the southern coast of Galicia, yielded a tetraprenyltoluquinol chromane meroditerpene compound known as 1b, whose structure is revised. The relative configuration of 1b was determined by J-based configurational methodology combined with an iJ/DP4 statistical analysis and further confirmed by measuring two anisotropic properties: carbon residual chemical shift anisotropies (13C-RCSAs) and one-bond 1H-13C residual dipolar couplings (1DCH-RDCs). The absolute configuration of 1b was deduced by ECD/OR/TD-DFT methods and established as 3R,7S,11R.

Statistical evaluation of simulated NMR data of flexible molecules

A new probability score-named χ-probability-is introduced for evaluating the fit of mixed NMR datasets to calculate molecular model ensembles, in order to answer challenging structural questions such as the determination of stereochemical configurations. Similar to the DP4 parameter, the χ-probability is based on Bayes theorem and expresses the probability that an experimental NMR dataset fits to a given individual within a finite set of candidate structures or configurations. Here, the χ-probability is applied to single out the correct configuration in four example cases, with increasing complexity and conformational mobility. The NMR data (which include RDCs, NOE distances and ³J couplings) are calculated from MDOC (Molecular Dynamics with Orientational Constraints) trajectories and are investigated against experimentally measured data. It is demonstrated that this approach singles out the correct stereochemical configuration with probabilities more than 98%, even for highly mobile molecules. In more demanding cases, a decisive χ-probability test requires that the datasets include high-quality NOE distances in addition to RDC values.

Conformational analysis and concentration detection of linuron: Spectroscopic NMR and SERS study

Linuron is a commonly used organic herbicide which is used in plant growth control. Due to its potential health concerns, the characterization and monitoring of linuron have been a subject of several studies. In this work, we employed nuclear magnetic resonance (NMR) and Raman spectroscopic techniques supported with the density functional theory (DFT) to investigate the conformational behavior and electronic aspects of linuron. The selective nuclear Overhauser effect (SelNOE) spectra confirmed that linuron exists predominantly in the anti configuration and is facilitated with a weak intramolecular hydrogen bonding between the acidic amide proton and oxygen of methoxy moiety. Quantum chemical results showed that the corresponding syn form of the molecule is 8.5 kcal/mol less stable. Further, the surface enhanced Raman scattering (SERS) technique using gold nanoparticles (AuNPs) was implemented as a potential spectroscopic protocol for the concentration monitoring of trace linuron. The Raman responses of four vibrational modes, namely CC stretching, CN stretching, N-H rocking and ring deformation, were successfully enhanced with an excellent linear concentration-intensity dependency. The aromatic CC stretching vibration at 1595 cm^-1 in the Raman spectra has demonstrated the highest enhancement factor (6.5 × 10⁴) and the lowest limit of detection (10^-7 M). The interaction of linuron with the gold nanocluster was simulated by establishing a simple DFT model which predicted that the most pronounced binding with the gold atom takes place at the benzene ring.

Exposing Hidden Conformations of Carbamazepine Appearing Due to Interaction With the Solid Phase by 2D 1H-15N HMBC NMR Spectroscopy

Two-dimensional ¹H-¹⁵N HMBC NMR spectra of the well-known anticonvulsant carbamazepine dissolved in different organic solvents, recorded on an NMR spectrometer prove the existence of hidden conformers in saturated solutions. Obtained conformer distribution arises due to the presence of the solid phase in saturated solution. A weak influence of ring currents was revealed for different molecular conformations of carbamazepine dissolved in a saturated solution, which provides a simple approach to discovering hidden conformations. Hidden conformers were found in three different solvents: dimethyl sulfoxide, chloroform, and dichloromethane.

Deuterium Residual Quadrupolar Couplings: Crossing the Current Frontiers in the Relative Configuration Analysis of Natural Products

The determination of the 3D structure (configuration and preferred conformation) of complex natural and synthetic organic molecules is a long-standing but still challenging task for chemists, with various implications in pharmaceutical sciences whether or not these substances have specific bioactivities. Nuclear magnetic resonance (NMR) in aligning media, either lyotropic liquid crystals (LLCs) or polymer gels, in combination with molecular modeling is a unique framework for solving complex structural problems whose analytical wealth lies in the establishment of nonlocal structural correlations. As an alternative to the already well-established anisotropic NMR parameters, such as RDCs (residual dipolar couplings) and RCSAs (residual chemical shift anisotropies), it is shown here that deuterium residual quadrupolar couplings (²H-RQCs) can be extracted from ²H 2D-NMR spectra recorded at the natural abundance level in samples oriented in a homopolypeptide LLCs (poly-γ-benzyl-l-glutamate (PBLG)). These ²H-RQCs were successfully used to address nontrivial structural problems in organic molecules. The performance and scope of this new tool is examined for two natural chiral compounds of pharmaceutical interest (strychnine and artemisinin). This is the first report in which the 3D structure/relative configuration of complex bioactive molecules is unambiguously determined using only ²H-RQCs, which, in this case, are at ²H natural abundance.

Reference-free NOE NMR analysis

Nuclear Overhauser Effect (NOE) methods in NMR are an important tool for 3D structural analysis of small molecules. Quantitative NOE methods conventionally rely on reference distances, known distances that have to be spectrally separated and are not always available. Here we present a new method for evaluation and 3D structure selection that does not require a reference distance, instead utilizing structures optimized by molecular mechanics, enabling NOE evaluation even on molecules without suitable reference groups.

A quantitative Nuclear Overhauser Effect (NOE) analysis approach that avoids the use of and internal reference distance to perform molecular configuration selection.

The simulation of NMR data of flexible molecules: sagittamide A as an example for MD simulations with orientational constraints

The recently developed MDOC (Molecular Dynamics with Orientational Constraints) simulation is applied for the first time to a fully flexible molecule. MDOC simulations aim to single out the naturally existing configuration of molecules and to elucidate conformer populations. The performance of the method was first demonstrated on a well-studied test case, the five-membered ring lactone (α-methylene-γ-butyrolactone). In the case of sagittamide A, one-bond ¹H-¹³C residual dipolar couplings (RDC) are used as orientational constraints that reorient the molecule or parts of it. In addition, NOE distances and ³J scalar couplings are used as constraints. Five possible configurations of sagittamide A (labelled a to e) are considered. One experimental RDC value per flexible unit was available and this was not sufficient to single out one valid configuration. The problem could be solved by including NOE distances as well as ³J couplings as complementary constraints into the MDOC simulations. In accordance with former investigations, we confirmed the configuration a for the natural product. A detailed analysis of conformers of the central chain of 6 chiral carbon atoms could be given by inspecting the MDOC trajectory. The relative abundance of these conformers is crucial in fulfilling all three sets of constraints.

Conformational Investigations in Flexible Molecules Using Orientational NMR Constraints in Combination with 3J-Couplings and NOE Distances

The downscaling of NMR tensorial interactions, such as dipolar couplings, from tens of kilohertz to a few hertz in low-order media is the result of dynamics spanning several orders of magnitudes, including vibrational modes (~ns-fs), whole-molecule reorientation (~ns) and higher barrier internal conformational exchange (<ms). In this work, we propose to employ these dynamically averaged interactions to drive an “alignment-tensor-free” molecular dynamic simulation with orientation constraints (MDOC) in order to efficiently access the conformational space sampled by flexible small molecules such as natural products. Key to this approach is the application of tensorial pseudo-force restraints which simultaneously guide the overall reorientation and conformational fluctuations based on defined memory function over the running trajectory. With the molecular mechanics force-field, which includes bond polarization theory (BPT), and complemented with other available NMR parameters such as NOEs and scalar J-couplings, MDOC efficiently arrives at dynamic ensembles that reproduce the entire NMR dataset with exquisite accuracy and theoretically reveal the systems conformational space and equilibrium. The method as well as its potential towards configurational elucidation is presented on diastereomeric pairs of flexible molecules: a small 1,4-diketone 1 with a single rotatable bond as well as a 24-ring macrolide related to the natural product mandelalide A 2.

Improving the accuracy of 1 H-19 F internuclear distance measurement using 2D 1 H-19 F HOESY

With the rise in fluorinated pharmaceuticals, it is becoming increasingly important to develop new ¹⁹ F NMR-based methods to assist in their analysis. Crucially, obtaining information regarding the conformational dynamics of a molecule in solution can aid the design of strongly binding therapeutics. Herein, we report the development of a 2D ¹ H-¹⁹ F Heteronuclear Overhauser Spectroscopy (HOESY) experiment to measure ¹ H-¹⁹ F internuclear distances, with accuracies of ~5% when compared with ¹ H-¹⁹ F internuclear distances calculated by quantum chemical methods. We demonstrate that correcting for cross-relaxation of ¹ H, using the diagonal peaks from the 2D ¹ H-¹ H Nuclear Overhauser Enhancement Spectroscopy (NOESY), is critical in obtaining accurate values for ¹ H-¹⁹ F internuclear distances. Finally, we show that by using the proposed method to measure ¹ H-¹⁹ F internuclear distances, we are able to determine the relative stereochemistry of two fluorinated pharmaceuticals.

Orientation and conformation of two [6]carbohelicenes in stretched polystyrene and a thermoresponsive polyaspartate

Two functionalized [6]carbohelicenes, one of which was also available in its two enantiomeric pure forms, were oriented in stretched polystyrene in CDCl₃ , and in a recently introduced chiral thermoresponsive lyotropic polyaspartate (poly(benzyl)_0.5 (phenethyl)_0.5 -L-aspartate) in C₂ D₂ Cl₄ . From the resulting ¹ H,¹³ C residual dipolar couplings, the helical pitch of a methylated [6]carbohelicene was determined and found to be in agreement with theoretical predictions and existing crystal structures (d(C2,C2') ≈ 4.3 Å). For a second [6]carbohelicene with para-methoxyphenyl substituents, a clear conformational preference of the substituents was observed. The orientational properties of the two helicene enantiomers in the chiral polyaspartate are very similar, but both drastically change around 306 K. We suggest this behavior is due to an unusual phase transition in the liquid crystal.

Polyketides from Marine-Derived Aspergillus porosus: Challenges and Opportunities for Determining Absolute Configuration

Fungal natural products have inspired and enabled countless modern therapeutics. During a survey of the secondary metabolites of endophytic fungi, we found that Aspergillus porosus produces new polyketides with interesting structural features named porosuphenols A-D (1, 2, 3a, and 3b). The structural elucidation of these metabolites was performed with 1D and 2D NMR techniques, Mosher ester analysis, J-based conformational analysis, and isotope exchange studies. The absolute configuration of these compounds was determined using typical approaches including comparative analysis of experimental NMR and electronic circular dichroism spectra with DFT calculations. However, these efforts did not provide conclusive results for porosuphenol A (1). To resolve this issue, we applied a strategy in which NMR data guide the conformer search. Herein are presented the structure elucidation of porosuphenols A-D as a case study in the challenges and opportunities for determination of absolute configuration. Lastly, bioassay-guided fractionation of cytotoxic fractions resulted in the additional isolation of pimarane diterpenes, sphaeropsidin A (4), and aspergiloid E (5).

Tricyclanos: conformationally constrained nucleoside analogues with a new heterotricycle obtained from a d-ribofuranose unit

A novel type of nucleoside analogue in which the sugar part is replaced by a new tricycle, 3,7,10-trioxa-11-azatricyclo[5.3.1.0^5,11]undecane has been prepared by substrate-controlled asymmetric synthesis. 1,5-Dialdehydes obtained from properly protected or unprotected uridine, ribothymidine, cytidine, inosine, adenosine and guanosine by metaperiodate oxidation reacted readily with tris(hydroxymethyl)aminomethane to provide the corresponding tricyclic derivatives with three new stereogenic centers. Through a double cyclisation cascade process the tricyclic compounds were obtained in good to high yields, with very high diastereoselectivity. Formation of one stereoisomer, out of the eight possible, was observed in all cases. The absolute configuration of the new stereotriad-containing tricyclic systems was aided by conventional NMR experiments followed by chemical shift calculations using an X-ray crystal structure as reference that was in good agreement with H-H distances obtained from a new ROESY NMR method. The synthesis was compatible with silyl, trityl and dimethoxytrityl protecting groups. A new reagent mixture containing ZnCl₂, Et₃SiH and hexafluoroisopropanol was developed for detritylation of the acid-sensitive tricyclano nucleosides.

Enhancing the utility of 1JCH coupling constants in structural studies through optimized DFT analysis

High accuracy for DFT-predicted ¹J_CH-couplings can be achieved without ad hoc corrections or empirical scaling by careful selection of the DFT method utilized for geometry optimization and J-coupling calculations.

Determination of the conformational states of strychnine in solution using NMR residual dipolar couplings in a tensor-free approach

Small molecules with rotatable bonds can occupy different conformational states in solution as a consequence of their thermal fluctuations. The accurate determination of the structures of such states, as well as of their statistical weights, has been challenging because of the technical difficulties in extracting information from experimental measurements, which are normally averaged over the conformational space available. Here, to achieve this objective, we present an approach based on a recently proposed tensor-free method for incorporating NMR residual dipolar couplings as structural restraints in replica-averaged molecular dynamics simulations. This approach enables the information provided by the experimental data to be used in the spirit of the maximum entropy principle to determine the structural ensembles of small molecules. Furthermore, in order to enhance the sampling of the conformational space we incorporated the metadynamics method in the simulations. We illustrate the method in the case of strychnine, determining the three major conformational states of this small molecule and their associated occupation probabilities.

Improved NOE fitting for flexible molecules based on molecular mechanics data – a case study with S-adenosylmethionine

Using the important biomolecule S-adenosyl methionine as an exemplar, we provide a new, enhanced approach for fitting MD data to high-accuracy NOE data, providing improvements in structure determination.

Importance of Rigidity in Designing Small Molecule Drugs To Tackle Protein-Protein Interactions (PPIs) through Stabilization of Desired Conformers

Tackling PPIs, particularly by stabilizing clinically favored conformations of target proteins, with orally available, bona fide small molecules remains a significant but immensely worthwhile challenge for the pharmaceutical industry. Success may be more likely through the application of nature's learnings to build intrinsic rigidity into the design of clinical candidates.

eNORA2 Exact NOE Analysis Program

We have recently developed an NMR protocol to extract exact distances between nuclei in proteins from an exact interpretation of NOESY buildup intensities (eNOEs). This enabled us to calculate multistate structural ensembles that exhibit realistic spatial sampling and long-range correlations. Our initial studies were laborious and required a deep understanding of the underlying spin dynamics. Here, we present a MatLab package that integrates all data processing steps required to convert intensities of assigned peaks in NOESY series into upper and lower distance limits for structure calculation. Those steps include organization of the data in object format, extraction of autorelaxation and cross-relaxation rate constants by fitting of diagonal peak decays and cross peak buildups, validation of the data, correction for spin diffusion, graphical display of the results, and generation of distance limits in CYANA compatible format. The analysis may be carried out using a full relaxation matrix or a simplified "divide and conquer" approach that allows for partial deuteration of protons. As the program does not require expertise beyond that of standard resonance assignment/structure calculation, it is suitable for experts and nonexperts alike.

Desktop NMR for structure elucidation and identification of strychnine adulteration

A complete assignment of the structure of strychnine with NMR spectroscopy at 1 T and identification of strychnine adulteration.

Extraction of distance restraints from pure shift NOE experiments

NMR techniques incorporating pure shift methods to improve signal resolution have recently attracted much attention, owing to their potential use in studies of increasingly complex molecular systems. Extraction of frequencies from these simplified spectra enables easier structure determination, but only a few of the methods presented provide structural parameters derived from signal integral measurements. In particular, for quantification of the nuclear Overhauser effect (NOE) it is highly desirable to utilize pure shift techniques where signal overlap normally prevents accurate signal integration, to enable measurement of a larger number of interatomic distances. However, robust methods for the measurement of interatomic distances using the recently developed pure shift techniques have not been reported to date. In this work we discuss some of the factors determining the accuracy of measurements of signal integrals in interferogram-based Zangger-Sterk (ZS) pure shift NMR experiments. The ZS broadband homodecoupling technique is used in different experiments designed for quantitative NOE determination from pure shift spectra. It is shown that the techniques studied can be used for quantitative extraction of NOE-derived distance restraints, as exemplified for the test case of strychnine.

Antimicrobial activity and cytotoxicity of polyketides isolated from the mushroom Xerula sp. BCC56836

Thirteen new polyketides (1, 3, 5–12, and 14–16) together with nine known compounds were isolated from the mushroom Xerula sp. BCC56836.