Use of Raman and Raman optical activity to extract atomistic details of saccharides in aqueous solution.

Sugars are crucial components in biosystems and industrial applications. In aqueous environments, the natural state of short saccharides or charged glycosaminoglycans is floating and wiggling in solution. Therefore, tools to characterize their structure in a native aqueous environment are crucial but not always available. Here, we show that a combination of Raman/ROA and, on occasions, NMR experiments with Molecular Dynamics (MD) and Quantum Mechanics (QM) is a viable method to gain insights into structural features of sugars in solutions. Combining these methods provides information about accessible ring puckering conformers and their proportions. It also provides information about the conformation of the linkage between the sugar monomers, i.e., glycosidic bonds, allowing for identifying significantly accessible conformers and their relative abundance. For mixtures of sugar moieties, this method enables the deconvolution of the Raman/ROA spectra to find the actual amounts of its molecular constituents, serving as an effective analytical technique. For example, it allows calculating anomeric ratios for reducing sugars and analyzing more complex sugar mixtures to elucidate their real content. Altogether, we show that combining Raman/ROA spectroscopies with simulations is a versatile method applicable to saccharides. It allows for accessing many features with precision comparable to other methods routinely used for this task, making it a viable alternative. Furthermore, we prove that the proposed technique can scale up by studying the complicated raffinose trisaccharide, and therefore, we expect its wide adoption to characterize sugar structural features in solution.

Unlocking the Hydrolytic Mechanism of GH92 α-1,2-Mannosidases: Computation Inspires the use of C-Glycosides as Michaelis Complex Mimics.

The conformational changes in a sugar moiety along the hydrolytic pathway are key to understand the mechanism of glycoside hydrolases (GHs) and to design new inhibitors. The two predominant itineraries for mannosidases go via O S2 →B2,5 →1 S5 and 3 S1 →3 H4 →1 C4 . For the CAZy family 92, the conformational itinerary was unknown. Published complexes of Bacteroides thetaiotaomicron GH92 catalyst with a S-glycoside and mannoimidazole indicate a 4 C1 →4 H5 /1 S5 →1 S5 mechanism. However, as observed with the GH125 family, S-glycosides may not act always as good mimics of GH's natural substrate. Here we present a cooperative study between computations and experiments where our results predict the E5 →B2,5 /1 S5 →1 S5 pathway for GH92 enzymes. Furthermore, we demonstrate the Michaelis complex mimicry of a new kind of C-disaccharides, whose biochemical applicability was still a chimera.

Silicon-bridged (1→1)-disaccharides: an umpoled glycomimetic scaffold.

Modification of the carbohydrate scaffold is an important theme in drug and vaccine discovery. Therefore, the preparation of novel types of glycomimetics is of interest in synthetic carbohydrate chemistry. In this manuscript, we present an early investigation of the synthesis, structure, and conformational behaviour of (1→1)-Si-disaccharides as a novel type of glycomimetics arising from the replacement of interglycosidic oxygen with a dimethyl-, methylpropyl-, or diisopropylsilyl linkage. We accomplished the preparation of this unusual group of umpoled compounds by the reaction of lithiated glycal or 2-oxyglycal units with dialkyldichlorosilanes. We demonstrated the good stability of the "Si-glycosidic" linkage under acidic conditions even at elevated temperatures. Next, we described the conformational landscape of these compounds by the combination of in silico modelling with spectroscopic and crystallographic methods. Finally, we explained the observed conformational flexibility of these compounds by the absence of gauche stabilizing effects that are typically at play in natural carbohydrates.

Functional stapled fragments of human preptin of minimised length.

Preptin is a 34-amino-acid-long peptide derived from the E-domain of a precursor of insulin-like growth factor 2 (pro-IGF2) with bone-anabolic and insulin secretion amplifying properties. Here, we describe the synthesis, structures, and biological activities of six shortened analogues of human preptin. Eight- and nine-amino-acid-long peptide amides corresponding to the C-terminal part of human preptin were stabilised by two types of staples to induce a higher proportion of helicity in their secondary structure. We monitored the secondary structure of the stapled peptides using circular dichroism. The biological effect of the structural changes was determined afterwards by the ability of peptides to stimulate the release of intracellular calcium ions. We confirmed the previous observation that the stabilisation of the disordered conformation of human preptin has a deleterious effect on biological potency. However, surprisingly, one of our preptin analogues, a nonapeptide stabilised by olefin metathesis between positions 3 and 7 of the amino acid chain, had a similar ability to stimulate calcium ions' release to the full-length human preptin. Our findings could open up new ways to design new preptin analogues, which may have potential as drugs for the treatment of diabetes and osteoporosis.

Electron Correlation or Basis Set Quality: How to Obtain Converged and Accurate NMR Shieldings for the Third-Row Elements?

The quality of theoretical NMR shieldings calculated at the quantum-chemical level depends on various theoretical aspects, of which the basis set type and size are among the most important factors. Nevertheless, not much information is available on the basis set effect on theoretical shieldings of the NMR-active nuclei of the third row. Here, we report on the importance of proper basis set selection to obtain accurate and reliable NMR shielding parameters for nuclei from the third row of the periodic table. All calculations were performed on a set of eleven compounds containing the elements Na, Mg, Al, Si, P, S, or Cl. NMR shielding tensors were calculated using the SCF-HF, DFT-B3LYP, and CCSD(T) methods, combined with the Dunning valence aug-cc-pVXZ, core-valence aug-cc-pCVXZ, Jensen polarized-convergent aug-pcSseg-n and Karlsruhe x2c-Def2 basis set families. We also estimated the complete basis set limit (CBS) values of the NMR parameters. Widely scattered nuclear shieldings were observed for the Dunning polarized-valence basis set, which provides irregular convergence. We show that the use of Dunning core-valence or Jensen basis sets effectively reduces the scatter of theoretical NMR results and leads to their exponential-like convergence to CBS. We also assessed the effect of vibrational, temperature, and relativistic corrections on the predicted shieldings. For systems with single bonds, all corrections are relatively small, amounting to less than 4% of the CCSD(T)/CBS value. Vibrational and temperature corrections were less reliable for H3PO and HSiCH due to the high anharmonicity of the molecules. An abnormally high relativistic correction was observed for phosphorus in PN, reaching ~20% of the CCSD(T)/CBS value, while the correction was less than 7% for other tested molecules.

Simulation of Raman and Raman optical activity of saccharides in solution.

Structural studies of sugars in solution are challenging for most of the traditional analytical techniques. Raman and Raman optical activity (ROA) spectroscopies were found to be extremely convenient for this purpose. However, Raman and ROA spectra of saccharides are challenging to interpret and model due to saccharides' flexibility and polarity. In this study, we present an optimized computational protocol that enables the simulation of the spectra efficiently. Our protocol, which results in good agreement with experiments, combines molecular dynamics and density functional theory calculations. It further uses a smart optimization procedure and a novel adaptable scaling function. The numerical stability and accuracy of individual computational steps are evaluated by comparing simulated and experimental spectra of d-glucose, d-glucuronic acid, N-acetyl-d-glucosamine, methyl ß-d-glucopyranoside, methyl ß-d-glucuronide, and methyl ß-N-acetyl-d-glucosaminide. Overall, our Raman and ROA simulation protocol allows one to routinely and reliably calculate the spectra of small saccharides and opens the door to advanced applications, such as complete 3-dimensional structural determination by direct interpretation of the experimental spectra.

Vibrational Structure in Magnetic Circular Dichroism Spectra of Polycyclic Aromatic Hydrocarbons.

Absorption and magnetic circular dichroism (MCD) spectroscopies are powerful and simple methods to discriminate among various compounds. Polycyclic aromatic hydrocarbons provide particularly strong signal, which, for example, facilitates their detection in the environment. However, interpretation of the spectra is often based on quantum-chemical simulations, providing a limited precision only. In the present work, we use time-dependent density functional theory and complete active space second-order perturbation theories to understand spectral features observed in a series of naphthalene, anthracene, phenanthrene, and three larger compounds. The electronic computations provided reasonable agreement with the experiment for the smaller molecules, while a large error persisted for the bigger ones. However, many discrepancies could be explained by vibrational splitting of the electronic transitions across the entire spectral range. Compared to plain absorption, MCD spectral bands and their vibrational splitting were more specific for each aromatic molecule. The computational tools allowing simulations of detailed vibrational features in the electronic spectra thus promise to open a qualitatively new chapter in the spectroscopy of aromatic compounds.

Properties of the Only Thorium Fullerene, Th@C84, Uncovered.

Only a single thorium fullerene, Th@C84, has been reported to date (Akiyama, K.; et al. J. Nucl. Radiochem. Sci. 2002, 3, 151-154). Although the system was characterized by UV-vis and XANES (X-ray absorption near edge structure) spectra, its structure and properties remain unknown. In this work we used the density functional calculations to identify molecular and electronic structure of the Th@C84. Series of molecular structures satisfying the ThC84 stoichiometric formula were studied comprising 24 IPR and 110 non-IPR Th@C84 isomers as well as 9 ThC2@C82 IPR isomers. The lowest energy structure is Th@C84-Cs(10) with the singlet ground state. Its predicted electronic absorption spectra are in agreement with the experimentally observed ones. The bonding between the cage and Th was characterized as polar covalent with Th in formal oxidation state IV. The NMR chemical shifts of Th@C84-Cs(10) were predicted to guide the future experimental efforts in identification of this compound.

On the magnetic circular dichroism of benzene. A density-functional study.

Spectroscopy of magnetic circular dichroism (MCD) provides enhanced information on molecular structure and a more reliable assignment of spectral bands than absorption alone. Theoretical modeling can significantly enhance the information obtained from experimental spectra. In the present study, the time dependent density functional theory is employed to model the lowest-energy benzene transitions, in particular to investigate the role of the Rydberg states and vibrational interference in spectral intensities. The effect of solvent is explored on model benzene-methane clusters. For the lowest-energy excitation, the vibrational sub-structure of absorption and MCD spectra is modeled within the harmonic approximation, providing a very good agreement with the experiment. The simulations demonstrate that the Rydberg states have a much stronger effect on the MCD intensities than on the absorption, and a very diffuse basis set must be used to obtain reliable results. The modeling also indicates that the Rydberg-like states and associated transitions may persist in solutions. Continuum-like solvent models are thus not suitable for their modeling; solvent-solute clusters appear to be more appropriate, providing they are large enough.

Simulation of Raman optical activity of multi-component monosaccharide samples.

Determination of the saccharide structure in solution is a laborious process that can be significantly enhanced by optical spectroscopies. Raman optical activity (ROA) spectra are particularly sensitive to the chirality and conformation. However, the interpretation of them is largely dependent on computational tools providing a limited precision only. To understand the limitations and the link between spectral shapes and the structure, in the present study we measured and interpreted using a combination of molecular dynamics (MD) and density functional theory (DFT) Raman and ROA spectra of glucose and mannose solutions. Factors important for analyses of mixtures of conformers, anomers, and different monosaccharides are discussed as well. The accuracy of the simulations was found to be strongly dependent on the quality of the hydration model; the dielectric continuum solvent model provided lower accuracy than averaging of many solvent-solute clusters. This was due to different conformer weighting rather than direct involvement of water molecules in scattering recorded as ROA. However, the cluster-based simulations also failed to correctly reproduce the ratios of principal monosaccharide forms. The best results were obtained by a combined MD/DFT simulation, with the ratio of α- and ß-anomers and the -CH2OH group rotamers determined experimentally by NMR. Then a decomposition of experimental spectra into calculated subspectra provided realistic results even for the glucose and mannose mixtures. Raman spectra decomposition provided a better overall accuracy (∼5%) than ROA (∼10%). The combination of vibrational spectroscopy with theoretical simulations represents a powerful tool for analysing the saccharide structure. Conversely, the ROA and Raman data can be used to verify the quality of MD force fields and other parameters of computational modeling.

Calculation of Raman parameters of real-size zigzag (n, 0) single-walled carbon nanotubes using finite-size models.

Structural and selected Raman features of pristine single-walled carbon nanotubes (SWCTNs) with diameters from 0.4 to 1.2 nm and total lengths up to 2.15 nm were studied using the density functional theory (DFT) at the UB3LYP/6-31G* level. Models of different lengths (1, 4, 6 and 10 adjacent bamboo-units) of zigzag (n, 0) SWCNTs, for n ranging from 5 to 15, were studied. Highly systematic changes of individual CC bond lengths and angles along the nanotube axis were observed and described for the longest models. Predicted Raman active radial breathing mode (RBM) vibrational frequencies regularly decreased upon increasing the nanotube diameter and only a negligible effect of the tube length was observed. The changes in calculated RBM frequencies with increasing diameter were close to values estimated using empirical formulas. The experimental G-mode characteristics were reasonably well reproduced using the 4-unit model, especially for tubes with the diameter d > 1 nm. Raman features were also determined for cyclacenes representing the shortest models of SWCNTs. Calculated RBM frequencies of cyclacenes match closely the values for longer SWCNT models but are too inaccurate in the case of the G-mode. For the first time, the Raman properties of SWCNTs were also determined using the Cartesian coordinate tensor (CCT) transfer technique, thus providing reasonable frequencies of Raman active bands for long tubes consisting of 10 bamboo-units.

On the origin of the electronic and magnetic circular dichroism of naphthyl C-glycosides: Anomeric configuration.

Aryl C-glycosides, in which the glycosidic bond is changed to a carbon-carbon bond, are an important family of biologically-active compounds. They often serve as secondary metabolites or exhibit antibiotic and cytostatic activities. Their stability to hydrolysis has made them attractive targets for new drugs. Their conformational behavior often strongly influences the resulting function. Their detailed structural and conformational description is thus highly desirable. This work studies the structure of three different naphthyl C-glycosides using UV-vis absorption as well as electronic and magnetic circular dichroism. It also describes their conformational preferences using a combination of molecular dynamics and DFT calculations. The reliability of these preferences has been verified by simulations of spectral properties and a comparison with their measured spectra. In particular, ECD spectroscopy has been shown to distinguish easily between α- and ß-pseudoanomers of aryl C-glycosides. Computer simulations and spectral decomposition have revealed how the resulting ECD patterns of the naphthyl glycosides studied are influenced by different conformer populations. In conclusion, reliable ECD patterns cannot be calculated by separating the naphthyl rotation from other conformational motions. MCD patterns have been similar for all the naphthyl C-glycosides studied. No clear diagnostic features have been found for either the pseudoanomeric configuration or the preferred hydroxymethyl rotamer. Nevertheless, the work has demonstrated the potential of MCD for the study of aryl glycosides interacting with proteins.

Solid-state vibrational circular dichroism for pharmaceutical applications: Polymorphs and cocrystal of sofosbuvir.

X-ray diffraction is a commonly used technique in the pharmaceutical industry for the determination of the atomic and molecular structure of crystals. However, it is costly, sometimes time-consuming, and it requires a considerable degree of expertise. Vibrational circular dichroism (VCD) spectroscopy resolves these limitations, while also exhibiting substantial sensitivity to subtle modifications in the conformation and molecular packaging in the solid state. This study showcases VCD's ability to differentiate between various crystal structures of the same molecule (polymorphs, cocrystals). We examined the most effective approach for producing high-quality spectra and unveiled the intricate link between structure and spectrum via quantum-chemical computations. We rigorously assessed, using alanine as a model compound, multiple experimental conditions on the resulting VCD spectra, with the aim of proposing an optimal and efficient procedure. The proposed approach, which yields reliable, reproducible, and artifact-free results with maximal signal-to-noise ratio, was then validated using a set comprising of three amino acids (serine, alanine, tyrosine), one hydroxy acid (tartaric acid), and a monosaccharide (ribose) to mimic active pharmaceutical components. Finally, the optimized approach was applied to distinguish three polymorphs of the antiviral drug sofosbuvir and its cocrystal with piperazine. Our results indicate that solid-state VCD is a prompt, cost-effective, and easy-to-use technique to identify crystal structures, demonstrating potential for application in pharmaceuticals. We also adapted the cluster and transfer approach to calculate the spectral properties of molecules in a periodic crystal environment. Our findings demonstrate that this approach reliably produces solid-state VCD spectra of model compounds. Although for large molecules with many atoms per unit cell, such as sofosbuvir, this approach has to be simplified and provides only a qualitative match, spectral calculations, and energy analysis helped us to decipher the observed differences in the experimental spectra of sofosbuvir.

Fullerene C70 characterization by 13C NMR and the importance of the solvent and dynamics in spectral simulations.

The nuclear magnetic resonance (NMR) spectroscopy combined with theoretical calculations is an important tool for fullerene identification. However, the accuracy of available theoretical methods is often not adequate. Therefore, in this work, different computational aspects needed to simulate realistically chemical shifts in the C70 molecule are investigated by density functional theory (DFT) calculations. The importance of the functional choice, basis set, solvent, and molecular motions was assessed. The solvent was simulated using the implicit conductor-like polarized continuum model. The molecular motions were included via anharmonic corrections and averaging of snapshots obtained from classical and first-principles molecular dynamics (MD) simulations. Comparison to experiment revealed that density functional calculations typically overestimate the (13)C NMR chemical shifts. Hybrid functionals, such as BHandH and BHandHLYP, and long-range corrected functionals, such as wB97xd and CAM-B3LYP, give the best results. While the solvent has a minor effect (chemical shift changes by ~1 ppm), the vibrational and dynamical effects are surprisingly large, causing changes up to 9 ppm. Consideration of the latter was also necessary to explain the observed temperature dependence. While the dynamical corrections for MD performed in vacuum were overestimated, inclusion of the solvent in simulations provided more realistic results. The study thus points out the importance of an appropriate solvent model and a complex approach to the modelling, balancing the static, dynamic and environmental factors.

3He NMR: from free gas to its encapsulation in fullerene.

The (3)He nuclear magnetic shieldings were calculated for single helium atom, its dimer, simple models of fullerene cages (He@Cn), and single wall carbon nanotubes. The performances of several levels of theory (HF, MP2, DFT-VSXC, CCSD, CCSD(T), and CCSDT) were tested. Two sets of polarization-consistent basis sets were used (pcS-n and aug-pcS-n), and an estimate of (3)He nuclear magnetic shieldings in the complete basis set limit using a two-parameter fit was established. Theoretical (3)He results reproduced accurately previously reported theoretical values for helium gas, dimer, and helium probe inside several fullerene cages. Excellent agreement with experimental values was achieved. (3)He nuclear magnetic shieldings of single helium atom approaching various points of benzene ring were tested, and an impact of (3)He confinement within fullerene cages of different size on the (3)He chemical shift was determined.

Modeling 21Ne NMR parameters for carbon nanosystems.

The potential of nuclear magnetic resonance (NMR) technique in probing the structure of porous systems including carbon nanostructures filled with inert gases is analysed theoretically using accurate calculations of neon ((21) Ne) nuclear magnetic shieldings. The CBS estimates of (21) Ne NMR parameters were performed for single atom, its dimer and neon interacting with acetylene, ethylene and 1,3-cyclopentadiene. Several levels of theory including restricted Hartree-Fock (RHF), Møller-Plesset perturbation theory to the second order (MP2), density functional theory (DFT) with van Voorhis and Scuseria's t-dependent gradient-corrected correlation functional (VSXC), coupled cluster with single and doubles excitations (CCSD), with single, doubles and triples included in a perturbative way (CCSD(T)) and single, doubles and tripes excitations (CCSDT) combined with polarization-consistent aug-pcS-n series of basis sets were employed. The impact of neon confinement inside selected fullerene cages used as an NMR probe was studied at the RHF/pcS-2 level of theory. A sensitivity of neon probe to the proximity of multiple CC bonds in C2 H2 , C2 H4 , C5 H6 and inside C28 , C30 , C32 , C34 and C60 fullerenes was predicted from (21) Ne NMR parameters' changes. Copyright © 2013 John Wiley & Sons, Ltd.

Estimation of isotropic nuclear magnetic shieldings in the CCSD(T) and MP2 complete basis set limit using affordable correlation calculations.

A linear correlation between isotropic nuclear magnetic shielding constants for seven model molecules (CH2 O, H2 O, HF, F2 , HCN, SiH4 and H2 S) calculated with 37 methods (34 density functionals, RHF, MP2 and CCSD(T)), with affordable pcS-2 basis set and corresponding complete basis set results, estimated from calculations with the family of polarization-consistent pcS-n basis sets is reported. This dependence was also supported by inspection of profiles of deviation between CBS estimated nuclear shieldings and shieldings obtained with the significantly smaller basis sets pcS-2 and aug-cc-pVTZ-J for the selected set of 37 calculation methods. It was possible to formulate a practical approach of estimating the values of isotropic nuclear magnetic shielding constants at the CCSD(T)/CBS and MP2/CBS levels from affordable CCSD(T)/pcS-2, MP2/pcS-2 and DFT/CBS calculations with pcS-n basis sets. The proposed method leads to a fairly accurate estimation of nuclear magnetic shieldings and considerable saving of computational efforts.

Recombinant Insulin-Like Growth Factor 1 Dimers: Receptor Binding Affinities and Activation Abilities.

Insulin-like growth factor 1 (IGF-1) and its IGF-1 receptor (IGF-1R) belong to an important biological system that is involved in the regulation of normal growth, but that has also been recognized as playing a role in cancer. IGF-1R antagonists could be interesting for the testing of their potential antiproliferative properties as an alternative to IGF-1R tyrosine-kinase inhibitors or anti-IGF-1R monoclonal antibodies. In this study, we were inspired by the successful development of insulin dimers capable of antagonizing insulin effects on the insulin receptor (IR) by simultaneous binding to two separated binding sites and by blocking structural rearrangement of the IR. We designed and produced in Escherichia coli three different IGF-1 dimers in which IGF-1 monomers are interlinked through their N- and C-termini, with linkers having 8, 15 or 25 amino acids. We found that the recombinant products were susceptible to the formation of misfolded or reduced variants, but that some of them were able to bind IGF-1R in low nanomolar affinities and all of them activate IGF-1R proportionally to their binding affinities. Overall, our work can be considered as a pilot study that, although it did not lead to the discovery of new IGF-1R antagonists, explored the possibility of recombinant production of IGF-1 dimers and led to the preparation of active compounds. This work could inspire further studies dealing, for example, with the preparation of IGF-1 conjugates with specific proteins for the study of the hormone and its receptor or for therapeutic applications. Supplementary Information: The online version contains supplementary material available at 10.1007/s10989-023-10499-1.

Formation of ibrutinib solvates: so similar, yet so different.

The transformation processes of non-solvated ibrutinib into a series of halogenated benzene solvates are explored in detail here. The transformation was studied in real time by X-ray powder diffraction in a glass capillary. Crystal structures of chlorobenzene, bromobenzene and iodobenzene solvates are isostructural, whereas the structure of fluorobenzene solvate is different. Four different mechanisms for transformation were discovered despite the similarity in the chemical nature of the solvents and crystal structures of the solvates formed. These mechanisms include direct transformations and transformations with either a crystalline or an amorphous intermediate phase. The binding preference of each solvate in the crystal structure of the solvates was examined in competitive slurry experiments and further confirmed by interaction strength calculations. Overall, the presented system and online X-ray powder diffraction measurement provide unique insights into the formation of solvates.

Non-glycosylated IGF2 prohormones are more mitogenic than native IGF2.

Insulin-like Growth Factor-2 (IGF2) is important for the regulation of human embryonic growth and development, and for adults' physiology. Incorrect processing of the IGF2 precursor, pro-IGF2(156), leads to the formation of two IGF2 proforms, big-IGF2(87) and big-IGF2(104). Unprocessed and mainly non-glycosylated IGF2 proforms are found at abnormally high levels in certain diseases, but their mode of action is still unclear. Here, we found that pro-IGF2(156) has the lowest ability to form its inactivating complexes with IGF-Binding Proteins and has higher proliferative properties in cells than IGF2 and other IGF prohormones. We also showed that big-IGF2(104) has a seven-fold higher binding affinity for the IGF2 receptor than IGF2, and that pro-IGF2(87) binds and activates specific receptors and stimulates cell growth similarly to the mature IGF2. The properties of these pro-IGF2 forms, especially of pro-IGF2(156) and big-IGF2(104), indicate them as hormones that may be associated with human diseases related to the accumulation of IGF-2 proforms in the circulation.