Computational NMR of Carbohydrates: Theoretical Background, Applications, and Perspectives

Synthesis and unexpected binding of monofluorinated N,N'-diacetylchitobiose and LacdiNAc to wheat germ agglutinin

Fluorination of carbohydrate ligands of lectins is a useful approach to examine their binding profile, improve their metabolic stability and lipophilicity, and convert them into 19F NMR-active probes. However, monofluorination of monovalent carbohydrate ligands often leads to a decreased or completely lost affinity. By chemical glycosylation, we synthesized the full series of methyl β-glycosides of N,N'-diacetylchitobiose (GlcNAcβ(1-4)GlcNAcβ1-OMe) and LacdiNAc (GalNAcβ(1-4)GlcNAcβ1-OMe) systematically monofluorinated at all hydroxyl positions. A competitive enzyme-linked lectin assay revealed that the fluorination at the 6'-position of chitobioside resulted in an unprecedented increase in affinity to wheat germ agglutinin (WGA) by one order of magnitude. For the first time, we have characterized the binding profile of a previously underexplored WGA ligand LacdiNAc. Surprisingly, 4'-fluoro-LacdiNAc bound WGA even stronger than unmodified LacdiNAc. These observations were interpreted using molecular dynamic calculations along with STD and transferred NOESY NMR techniques, which gave evidence for the strengthening of CH/π interactions after deoxyfluorination of the side chain of the non-reducing GlcNAc. These results highlight the potential of fluorinated glycomimetics as high-affinity ligands of lectins and 19F NMR-active probes.

Liquid-phase NMR of asphaltenes

The present review focuses on the most recent advances in liquid-phase NMR of asphaltenes, leaving apart an overwhelming amount of publications dealing with solid-state NMR investigations in this field. Owing to the complexity of the coal-derived products, and in particular, asphaltenes, their 1H and 13C NMR spectra consist of a number of overlapping signals belonging to different hydrocarbon types. Comprehensive studies of asphaltenes by means of NMR reveal the characteristic functional groups of their fractions together with the spectral regions in which they resonate. NMR studies of asphaltenes provide a straightforward guideline for their chemical composition and that of the related coal-derived products.

MA'AT Analysis: Probability Distributions of Molecular Torsion Angles in Solution from NMR Spectroscopy

ConspectusMonosaccharides adopt multiple conformations in solution, and this structural complexity increases significantly when they are assembled into oligosaccharides and polysaccharides. Characterization of the conformational properties of saccharides in solution by NMR spectroscopy has been hampered by several complicating factors, including difficulty interpreting spectra because of significant signal overlap, population averaging of NMR parameters, and unique properties of the spectra that make accurate measurements of NMR parameters prone to error (e.g., non-first-order effects on J-couplings). Current conformational assignments rely heavily on theoretical calculations, especially molecular dynamics (MD) simulations, to interpret the experimental NMR parameters. While these studies assert that the available experimental data fit the calculated models well, a lack of independent experimental validation of the force fields from which MD models are derived and an inability to test all possible models that might be compatible with the experimental data in an unbiased manner make the approach less than ideal.NMR spin couplings or J-couplings have been used as structure constraints in organic and other types of molecules for more than six decades. The dihedral angle dependence of vicinal (three-bond) 1H-1H spin couplings (3JHH) first described by Karplus led to an explosion of applications for a wide range of conformational problems. Other vicinal J-couplings (e.g., 3JCCOP, 3JHCOP, and 3JCOCH) have been found to exhibit similar dihedral angle dependencies. 3J values have been used to assign the preferred conformation in molecules that are conformationally homogeneous. However, many molecules, particularly those in biological systems, are conformationally flexible, which complicates structural interpretations of J values in solution. Three-state staggered models are often assumed in order to deconvolute the conformationally averaged J values into conformer populations. While widely applied, this approach assumes highly idealized models of molecular torsion angles that are likely to be poor representations of those found in solution. In addition, this treatment often gives negative populations and neglects the presence of librational averaging of molecular torsion angles.Recent work in this research group has focused on the development of a hybrid experimental-computational method, MA'AT analysis, that provides probability distributions of molecular torsion angles in solution that can be superimposed on those obtained by MD. Ensembles of redundant NMR spin couplings, including 3J (vicinal), 2J (geminal), and sometimes 1J (direct) values, are used in conjunction with circular statistics to provide single- and multistate models of these angles. MA'AT analysis provides accurate mean torsion angles and circular standard deviations (CSDs) of each mean angle that describe the librational motion about the angle. Both conformational equilibria and dynamics are revealed by the method. In this Account, the salient features of MA'AT analysis are discussed, including some applications to conformational problems involving saccharides and peptides.

17 O nuclear magnetic resonance: Recent advances and applications

The present review is focused on the most recent achievements in the application of liquid phase 17 O nuclear magnetic resonance (NMR) to inorganic, organic, and biochemical molecules focusing on their structure, conformations, and (bio)chemical behavior. The review is composed of four basic parts, namely, (1) simple molecules; (2) water and hydrogen bonding; (3) metal oxides, clusters, and complexes; and (4) biological molecules. Experimental 17 O NMR chemical shifts are thoroughly tabulated. They span a range of as much as almost 650 ppm (from -35.6 to +610.0 ppm) for inorganic and organic molecules, whereas this range is much wider for biological species being of about 1350 ppm (from -12 to +1332 ppm), and in the case of hemoproteins and heme-model compounds, isotropic chemical shifts of up to 2500 ppm were observed. The general prospects and caveats in the modern development of the liquid phase 17 O NMR in chemistry and biochemistry are critically discussed and briefly outlined in view of their future applications.

Tritium NMR: A compilation of data and a practical guide

The present review is focused on experimental methods and structural applications of tritium NMR. It consists of five parts covering accordingly, introduction, brief overview, early (based on the papers appearing before 2000), more recent (based on the papers appeared in the interim of 2000 to 2015), and recent (based on the papers that appeared after 2015) reports. A special interest in this review is focused on practical aspects of tritium NMR spectroscopy, which is thoroughly illustrated by its numerous applications in chemistry and biochemistry.

Four new resin glycosides, calyhedins VII-X, from the rhizomes of Calystegia hederacea

Four new resin glycosides with macrolactone structures (jalapins), namely, calyhedins VII (1)-X (4), were isolated from the rhizomes of Calystegia hederacea Wall. (Convolvulaceae). The structures of 1-4 were determined based on spectroscopic data. They were classified into three ring types: a 27-membered ring (1), a 22-membered ring (2, 3), and a 23-membered ring (4). Their sugar moieties were partially acylated using five organic acids, including (E)-2-methylbut-2-enoic acid, 2S-methylbutyric acid, and 2 R-methyl-3R-hydroxybutyric acid. Compound 4 was the first genuine resin glycoside with calyhedic acid F as the glycosidic acid component. Additionally, the cytotoxic activities of 1, 2, and 4 towards HL-60 human promyelocytic leukaemia cells were evaluated. All compounds demonstrated almost the same activity as the positive control, cisplatin.

Computational NMR of carbohydrates: 1. Glucopyranoses

A high-level calculation of ¹ H and ¹³ C NMR chemical shifts of α- and β-d-glucopyranoses is carried out at the DFT level with taking into account their conformational composition to reveal the most effective computational protocols. A number of dedicated DFT functionals in combination with Jensen's pcS-n (n = 0-4) family of basis sets were applied to evaluate the most reliable combination. It was found that BHandHLYP/pcS-2 provided the most accurate and reliable computational protocol. Based on the performed calculations, the established computational protocol is generally recommended for the calculation of ¹ H and ¹³ C NMR chemical shifts of a wide series of carbohydrates.

Synthesis of 4-thio-d-glucopyranose and interconversion to 4-thio-d-glucofuranose

Sulfur containing glycosides offer an exciting prospect for inclusion within noncanonical glycan sequences, particularly as enabling probes for chemical glycobiology and for carbohydrate-based therapeutic development. In this context, we required access to 4-thio-d-glucopyranose and sought its chemical synthesis. Unable to isolate this material in homogenous form, we observed instead a thermodynamic preference for interconversion of the pyranose to 4-thio-d-glucofuranose. Accordingly, we present an improved method to access both bis(4-thio-d-glucopyranoside)-4,4'-disulfide and 4-thio-d-glucofuranose from a single precursor, demonstrating that the latter compound can be accessed from the former using a dithiothreitol controlled reduction of the disulfide. The dithiothreitol-mediated interconversion between pyranose (monomer and disulfide) and furanose forms for this thiosugar is monitored by ¹H NMR spectroscopy over a 24-h period. Access to these materials will support accessing sulfur-containing mimetics of glucose and derivatives therefrom, such as sugar nucleotides.

The impact of conformational sampling on first-principles calculations of vicinal COCH J-couplings in carbohydrates

Dihedral angles in organic molecules and biomolecules are vital structural parameters that can be indirectly probed by nuclear magnetic resonance (NMR) measurements of vicinal J-couplings. The empirical relations that map the measured couplings to dihedral angles are typically determined by fitting using static structural models, but this neglects the effects of thermal fluctuations at the finite temperature conditions under which NMR measurements are often taken. In this study, we calculate ensemble-averaged J-couplings for several structurally rigid carbohydrate derivatives using first-principles molecular dynamics simulations to sample the thermally accessible conformations around the minimum energy structure. Our results show that including thermal fluctuation effects significantly shifts the predicted couplings relative to single-point calculations at the energy minima, leading to improved agreement with experiments. This provides evidence that accounting for conformational sampling in first-principles calculations can improve the accuracy of NMR-based structure determination for structurally complex carbohydrates.

Computational 1 H and 13 C NMR in structural and stereochemical studies

Present review outlines the advances and perspectives of computational ¹ H and ¹³ C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational ¹ H and ¹³ C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.

MA'AT: A Web-Based Application to Determine Rotamer Population Distributions in Solution from Nuclear Magnetic Resonance Spin-Coupling Constants

A hybrid experimental-computational method to determine conformational equilibria of molecules in solution has been developed based on the use of redundant nuclear magnetic resonance (NMR) spin-spin coupling constants (spin-couplings; J-couplings), density functional theory (DFT) calculations, and circular statistics. The mathematics that underpins the method, known as MA'AT analysis, is presented, and key components of a computer program that applies this algorithm are discussed. The method was tested using single-state and multi-state models to identify the factors required to obtain reliable results, to establish the limitations of the method, and to highlight techniques to evaluate the uniqueness of solution.

Efficiently Computing NMR 1H and 13C Chemical Shifts of Saccharides in Aqueous Environment

Determining the structure of saccharides in their native environment is crucial to understanding their function and more accurately targeting their utilization. Nuclear magnetic resonance observables such as the nuclear Overhauser effect or spin-spin coupling constants are routinely utilized to study saccharides in their native water environment. However, while highly sensitive to the local environment, chemical shifts are mostly overlooked, despite being commonly measured for compounds identification. Although chemical shifts carry considerable structural information, their direct association with structure is notoriously difficult. This is mostly due to the similarity in the chemical nature of most saccharides causing similar physicochemical environments close to sugar C and H atoms, resulting in comparable chemical shifts. The rise of computational power allows one to compute reliable chemical shifts and use them to determine atomistic details of these sugars in solution. However, any prediction is severely limited by the computational protocol used and its accuracy. In this work, we studied a set of 31 saccharides on which we evaluated various computational protocols to calculate the total number of 375 ¹H and 327 ¹³C chemical shifts of sugars in an aqueous environment. Our study proposes two cost-effective protocols for simulating ¹H and ¹³C chemical shifts that we recommend for further use. These protocols can help with the interpretation of experimental spectra, but we also show that they are also capable of structure prediction independently. This is possible because of the low mean absolute deviations of calculated shifts from the experiment (0.06 ppm for ¹H and 1.09 ppm for ¹³C). We explore different solvation methods, basis sets, and optimization schemes to reach such accuracy. A correct sampling of the conformation phase space of flexible sugar molecules is also key to obtaining accurately converged theoretical chemical shifts. The linear regression method was applied to convert the calculated isotropic nuclear magnetic shielding constants to simulated chemical shifts comparable with the experiment. The achieved level of accuracy can help in utilizing chemical shifts for elucidating the 3D atomistic structure of saccharides in aqueous solutions. All linear regression parameters obtained on our extensive set of sugars for all the tested protocols can be reutilized in future works.

Quantum Chemical Approaches to the Calculation of NMR Parameters: From Fundamentals to Recent Advances

Quantum chemical methods for the calculation of indirect NMR spin–spin coupling constants and chemical shifts are always in progress. They never stay the same due to permanently developing computational facilities, which open new perspectives and create new challenges every now and then. This review starts from the fundamentals of the nonrelativistic and relativistic theory of nuclear magnetic resonance parameters, and gradually moves towards the discussion of the most popular common and newly developed methodologies for quantum chemical modeling of NMR spectra.

Computational NMR of natural products: On the way to super large molecules exemplified with alasmontamine A

¹ H and ¹³ C nuclear magnetic resonance (NMR) chemical shifts of a tetrakis monoterpene indole alkaloid alasmontamine A with a molecular formula of C₈₄ H₉₁ N₈ O₁₂ have been calculated at the PBE0/pcSseg-2//pcseg-2 level of theory on M06-2X/aug-cc-pVDZ geometry. In the course of the preliminary conformational search, six true minimum energy conformers were identified that can contribute to the actual conformation of this huge alkaloid. Calculated chemical shifts generally demonstrated a good agreement with available experimental data characterized with a corrected mean absolute error of 0.10 ppm for the range of about 7 ppm for protons and 1.1 ppm for the range of about 160 ppm for carbons.

Combined Computational NMR and Molecular Docking Scrutiny of Potential Natural SARS-CoV-2 Mpro Inhibitors

In continuation of the search for potential drugs that inhibit the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in this work, a combined approach based on the modeling of NMR chemical shifts and molecular docking is suggested to identify the possible suppressors of the main protease of this virus among a number of natural products of diverse nature. Primarily, with the aid of an artificial neural network, the problem of the reliable determination of the stereochemical structure of a number of studied compounds was solved. Complementary to the main goal of this study, theoretical modeling of NMR spectral parameters made it feasible to perform a number of signal reassignments together with introducing some missing NMR data. Finally, molecular docking formalism was applied to the analysis of several natural products that could be chosen as prospective candidates for the role of potential inhibitors of the main protease. The results of this study are believed to assist in further research aimed at the development of specific drugs based on the natural products against COVID-19.

Computational NMR of charged systems

This review covers NMR computational aspects of charged systems-carbocations, heterocations, and heteroanions, which were extensively studied in a number of laboratories worldwide, first of all, at the Loker Hydrocarbon Research Institute in California directed for several decades by a distinguished scientist, the Nobel laureate George Andrew Olah. The first part of the review briefly outlines computational background of the modern theoretical methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the historical results, advances, and perspectives of the computational NMR of classical carbocations like methyl cation, CH₃⁺ , and protonated methane, CH₅⁺ , together with their numerous homologs and derivatives. The third and the forth parts of this survey are focused on the NMR computational aspects of accordingly, heterocations and heteroanions, the organic and inorganic ions with a charge localized mainly on heteroatoms like boron, oxygen, nitrogen, and heavier elements.

The Flexibility of Oligosaccharides Unveiled Through Residual Dipolar Coupling Analysis

The intrinsic flexibility of glycans complicates the study of their structures and dynamics, which are often important for their biological function. NMR has provided insights into the conformational, dynamic and recognition features of glycans, but suffers from severe chemical shift degeneracy. We employed labelled glycans to explore the conformational behaviour of a β(1-6)-Glc hexasaccharide model through residual dipolar couplings (RDCs). RDC delivered information on the relative orientation of specific residues along the glycan chain and provided experimental clues for the existence of certain geometries. The use of two different aligning media demonstrated the adaptability of flexible oligosaccharide structures to different environments.