Theoretical calculations of 1H NMR chemical shifts for nitrogenated compounds in chloroform solution

Quantum Chemical NMR Spectroscopic Structural Analysis in Solution: The Investigation of 3-Indoleacetic Acid Dimer Formation in Chloroform and DMSO Solution

We present a DFT-PCM NMR study of 3-indoleacetic acid (3-IAA), used as a working example, including explicit solvent molecules, named PCM-nCHCl3, PCM-nDMSO (n = 0, 2, 4, 8, 14, 20, and 25), to investigate the dimer formation in solution. Apart from well-known cyclic (I) and open (II) acetic acid (AA) dimers, two new structures were located on DFT-PCM potential energy surface (PES) for 3-IAA named quasicyclic A (III) and quasicyclic B (IV), the last one having N-H…O hydrogen bond (instead of O-H…O). In addition, four other structures having π-π type interactions named V, VI, VII, and VIII were also obtained completing the sample on the PES. Our theoretical results and experimental 1H NMR data (CDCl3) strongly indicate that 3-IAA should exist in a quasicyclic form (III) in a chloroform solution different from AA. Solute-solvent interactions play a key role in O-H and N-H chemical shifts. The strong H-bond formation between the S=O and O-H and N-H groups produces large chemical shift value THAT masquerades the identification of dimer formation in DMSO solution based on 1H NMR chemical shift changes. However, analysis of 13C NMR and relative energy DFT-PCM-nDMSO results strongly indicate the presence of parallel ring interacting dimer having OH…benzene ring bond (VI). There can be a competition between solute-solute and solute-solvent interactions, and polar DMSO solvent can break the quasicyclic dimers (III and IV) intermolecular O-H…O and N-H…O bonds yielding two solvated monomeric species hydrogen bonded to O=S(CH3)2 groups, what may take place for other organic molecules in solution. However, it did not happen for the π-π interacting dimers and structure VI survived in DMSO solution.

Modeling Solvent Effects in Quantum Chemical Calculation of Relative Energies and NMR Chemical Shifts for Azithromycin

This work presents an investigation into the effect of including explicit solvent molecules in DFT (Density Functional Theory) calculations of relative energies (ΔErel) and NMR (Nuclear Magnetic Resonance) chemical shifts for organic molecules in chloroform, water, and dimethyl sulfoxide (DMSO) solution using the PCM (Polarizable Continuum Model) approach. The large and flexible molecule of the antibiotic azithromycin (AZM) containing five OH groups and other polar centers susceptible to interacting with solvent molecules was used here as a working example. An increasing number of explicit solvent molecules was used in the geometry optimization of the supermolecule (n = 5, 15, 25, and 50), which accurately reproduces the first solvation shell. We optimized a large AZM trimer (3AZM-75CHCl3) structure at the ωB97x-D/6-31G(d,p)-PCM level, containing 747 atoms, which may roughly simulate a 0.1 M dilute solution, with a good agreement with experimental NMR data. The supermolecule approach offers a robust description of solute-solvent intermolecular interactions, effectively accounting for both short- and long-range effects, making it a reliable method for selecting the predominant conformer in solution. While the effect of including explicit solvent molecules on the DFT calculation of ΔErel and 1H NMR chemical shifts (OH protons) is remarkable, it is only moderate for the evaluation of 13C NMR spectra, providing support for the use of the continuum solvation model in this case. For highly solvated structures, a degree of arbitrariness in the calculation of relative energies is naturally introduced, mainly due to solvent-solvent interaction, causing a strong dependence of total energies on the initial guess structure used in the geometry optimization procedure, with variation in ΔErel around 70 kcal mol-1 being predicted, and, therefore, it may not be quite suitable as a criterion to find the predominant conformer in solution. This does not happen with the DFT calculation of 1H NMR chemical shifts (RMSD variations less than 0.1 ppm were observed for distinct initial guess structures), which are more strongly influenced by the local chemical environment. This is an interesting result regarding the use of an explicit solvent model in DFT calculations for organic molecules.

Fluorenone-naphthyl encapsulated dual sensor for recognition of F- and Hg2+: Syngenetic effect with drug sobisis and molecular docking studies

A novel fluorenone-naphthyl pendant sensor (FTU) possessing thiourea functionality has been synthesized via a simple condensation method and utilized for the recognition of F- and Hg2+ ions in the solution of CH3CN. The addition of F- and Hg2+ ions to the FTU solution led to the appearance of red-shifted absorption bands at 340 and 315 nm, respectively. On the other hand, in the fluorescence spectrum, the two-fold decrease in fluorescence intensity of probe FTU was observed with F- ions; while complete quenching of the fluorescence intensity was noticed with Hg2+ ions at 423 nm. The limit of detection values of F- and Hg2+ ions were found to be 1.02 & 29.1 nM, respectively, measured by UV-vis studies and 0.0185 & 0.81 nM, respectively, measured by fluorescence studies, which are less than recommended by WHO. DFT computational assessments and 1H NMR titration experiments pointed to F- induced deprotonation of thiourea NH signals. However, the chelation-enhanced quenching effect (CHEQ) was held responsible for fluorescence quenching with Hg2+ addition. Moreover, the in-situ formed FTU + F- complex was utilized for secondary sensing of drug sobisis. Furthermore, the real-world applicability of sensor FTU has been successfully scrutinized for the recognition of F- ions in the toothpaste samples. In addition, molecular docking studies revealed that FTU exhibited excellent antibacterial potency towards different gram-positive as well as negative strains.

Modeling solvent effects and convergence of 31P-NMR shielding calculations with COBRAMM

Solvent effects on 31P-NMR parameters for triphenylphosphine oxide and triphenylphosphine in chloroform have been extensively investigated by testing different solvation models. The solvent is described implicitly, mixed implicitly/explicitly, and using full explicit models. Polarizable continuum model (PCM), molecular dynamic (MD) simulations, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations are used to disclose the effects of solute/solvent interactions and, more generally, the role of the embedding in NMR simulations. The results show the beneficial effect of carrying out QM/MM optimizations on top of geometries directly extracted from classical MD simulations, used to ensure representative conformational sampling. The nuclear shielding convergence has been tested against a different number of snapshots and with the inclusion of solvent shells into the QM region. An automated MD//QM/MM//GIAO protocol, implemented in the COBRAMM package, is here proposed and tested on trimethyl phosphite showing that our approach boosts the convergence of nuclear shielding satisfactorily. The present work aims to be a stepping-stone to assess proper QM/MM computational strategies in simulating chemical shifts in non-homogeneous systems like supramolecular and biological systems.

On the use OF 1H-NMR chemical shifts and thermodynamic data for the prediction of the predominant conformation of organic molecules in solution: the example of the flavonoid rutin

Conformational analyses of organic compounds in solution still represent a challenge to be overcome. The traditional methodology uses the relative energies of the conformations to decide which one is most likely to exist in the experimental sample. The goal of this work was to deepen the approach of conformational analysis of flavonoid rutin (a well-known antioxidant agent) in DMSO solution. The methodology we used in this paper involves expanding the sample configuration space to a total of 44 possible geometries, using Molecular Dynamics (MD) simulations, which accesses structures that would hardly be considered with our chemical perception, followed by DFT geometry optimizations using the ωB97X-D/6-31G(d,p) - PCM level of theory. Spectroscopic and thermodynamic analyses were done, by calculating the relative energies and nuclear magnetic resonance (1H-NMR) chemical shifts, comparing the theoretical and experimental 1H-NMR spectra (DMSO-d 6) and evaluating Mean Absolute Error (MAE). The essence of this procedure lies in searching for patterns, like those found in traditional DNA tests common in healthcare. Here, the theoretical spectrum plays the role of the analyzed human sample, while the experimental spectrum acts as the reference standard. In solution, it is natural for the solute to dynamically alter its geometry, going through various conformations (simulated here by MD). However, our DFT/PCM results show that a structure named 32 with torsion angles ϕ 1 and ϕ 2 manually rotated by approx. 20° showed the best theoretical-experimental agreement of 1H-NMR spectra (in DMSO-d 6). Relative energies benchmarking involving 16 DFT functionals revealed that the ωB97X-D is very adequate for estimating energies of organic compounds with dispersion of charge (MAE < 1.0 kcal mol-1, using ab initio post-Hartree-Fock MP2 method as reference). To describe the stability of the conformations, calculations of Natural Bonding Orbitals (NBO) were made, aiming to reveal possible intramolecular hydrogen bonds that stabilize the structures. Since van der Waals (vdW) interactions are difficult to be identified by NBO donations, the Reduced Density Gradient (RDG) were calculated, which provides 2D plots and 3D surfaces that describe Non-Covalent Interactions (NCI). These data allowed us to analyze the effect of dispersion interactions on the relative stability of the rutin conformations. Our results strongly indicate that a combination of DFT (ωB97X-D)-PCM relative energies and NMR spectroscopic criterion is a more efficient strategy in conformational analysis of organic compounds in solution.

The accuracy limit of chemical shift predictions for species in aqueous solution

Interpreting NMR experiments benefits from first-principles predictions of chemical shifts. Reaching the accuracy limit of theory is relevant for unambiguous structural analysis and dissecting theoretical approximations. Since accurate chemical shift measurements are based on using internal reference compounds such as trimethylsilylpropanesulfonate (DSS), a detailed comparison of experimental with theoretical data requires simultaneous consideration of both target and reference species ensembles in the same solvent environment. Here we show that ab initio molecular dynamics simulations to generate liquid-state ensembles of target and reference compounds, including explicitly their short-range solvation environments and combined with quantum-mechanical solvation models, allows for predicting highly accurate 1H (∼0.1-0.5 ppm) and aliphatic 13C (∼1.5 ppm) chemical shifts for aqueous solutions of the model compounds trimethylamine N-oxide (TMAO) and N-methylacetamide (NMA), referenced to DSS without any system-specific adjustments. This encompasses the two peptide bond conformations of NMA identified by NMR. The results are used to derive a general-purpose guideline set for predictive NMR chemical shift calculations of NMA in the liquid state and to identify artifacts of force field models. Accurate predictions are only obtained if a sufficient number of explicit water molecules is included in the quantum-mechanical calculations, disproving a purely electrostatic model of the solvent effect on chemical shifts.

Solvent- and functional-group-assisted tautomerism of 3-alkyl substituted 5-(2-pyridyl)-1,2,4-triazoles in DMSO-water

The tautomerism of a series of 5-alkyl substituted 3-(2-pyridyl)-1,2,4-triazoles in DMSO-d6-containing water has been investigated by 1H, 13C and 15N NMR spectroscopy. The populations of the three possible regioisomers in the tautomeric equilibrium (A [3-alkyl-5-(2-pyridyl)-1H], B [5-alkyl-3-(2-pyridyl)-1H] and C [5-alkyl-3-(2-pyridyl)-4H]) were determined. Isomers A (17-40%) and B (54-79%) are the major components and their ratio is insensitive to the substitution pattern, except for the unsubstituted and the methoxymethyl substituted derivatives. The isomer C (3-5%) has been fully characterised for the first time by NMR spectroscopy. Activation energies of tautomerisation (14.74-16.78 kcal mol-1) were determined by EXSY experiments, which also supported the involvement of water in the tautomerisation. Substituent effects on the 15N chemical shifts are relatively small. The DFT study of the tautomerism in DMSO-water showed that both A/B and B/C interconversions are assisted by the pyridine substituent and catalysed by solvent molecules. The NH-A/NH-B tautomerisation takes place via a relayed quadruple proton transfer mediated by three water molecules in the hydrogen-bonded cyclic substructure of a triazole·4H2O complex. The equilibrium B ⇄ C involves three steps: NH-B transfer to the pyridyl nitrogen mediated by a water molecule in a 1 : 1 cyclic complex, rotamerisation to bring the pyridinium NH close to N4 of the triazole catalysed by complexation to a DMSO molecule and transfer of the NH from the pyridinium donor to the N4 acceptor via a 1 : 1 complex with a bridging water molecule. This mechanism of 1,3-prototropic shift in triazoles is unprecedented in the literature.

Quantum Chemical Investigation of the Interaction of Thalidomide Monomeric, Dimeric, Trimeric, and Tetrameric Forms with Guanine DNA Nucleotide Basis in DMSO and Water Solution: A Thermodynamic and NMR Spectroscopy Analysis

Thalidomide (TLD) was used worldwide as a sedative, but it was revealed to cause teratogenicity when taken during early pregnancy. It has been stated that the (R) enantiomer of TLD has therapeutic effects, while the (S) form is teratogenic. Clinical studies, however, demonstrated the therapeutic efficacy of thalidomide in several intractable diseases, so TLD and its derivatives have played an important role in the development and therapy of anticancer drugs. Therefore, it is important to know the molecular mechanism of action of the TLD, although this is still not clear. In what molecular interactions are concerned, it is known that drug molecules can interact with DNA in different ways, for example, by intercalation between base pairs. Furthermore, the ability of the TLD to interact with DNA has been confirmed experimentally. In this work, we report a theoretical investigation of the interaction of the R and S enantiomers of TLD, in its monomeric, dimeric, trimeric, and tetrameric forms, with guanine (GUA) DNA nucleotide basis in solution using density functional theory (DFT). Our initial objective was to evaluate the interaction of TLD-R/S with GUA through thermodynamic and spectroscopic study in dimethyl sulfoxide (DMSO) solvent and an aqueous solution. Comparison of the experimental 1H nuclear magnetic resonance (NMR) spectrum in DMSO-d6 solution with calculated DFT-PCM-DMSO chemical shifts revealed that TLD can undergo molecular association in solution, and interaction of its dimeric form with a DNA base ((TLD)2-GUA and (TLD)2-2GUA, for example) through H-bond formation is likely to take place. Our results strongly indicated that we must consider the plausibility of the existence of TLD associations in solution when modeling the complexation of the TLD with biological targets. This is new information that may provide further insight into our understanding of drug binding to biological targets at the molecular level.

Quantum chemical investigation of predominant conformation of the antibiotic azithromycin in water and DMSO solutions: thermodynamic and NMR analysis

Azithromycin (AZM) is a macrolide-type antibiotic used to prevent and treat serious infections (mycobacteria or MAC) that significantly inhibit bacterial growth. Knowledge of the predominant conformation in solution is of fundamental importance for advancing our understanding of the intermolecular interactions of AZM with biological targets. We report an extensive density functional theory (DFT) study of plausible AZM structures in solution considering implicit and explicit solvent effects. The best match between the experimental and theoretical nuclear magnetic resonance (NMR) profiles was used to assign the preferred conformer in solution, which was supported by the thermodynamic analysis. Among the 15 distinct AZM structures, conformer M14, having a short intramolecular C6-OH … N H-bond, is predicted to be dominant in water and dimethyl sulfoxide (DMSO) solutions. The results indicated that the X-ray structure backbone is mostly conserved in solution, showing that large flexible molecules with several possible conformations may assume a preferential spatial orientation in solution, which is the molecular structure that ultimately interacts with biological targets.

FTIR study on the CO interactions of benzeneacetamide in solution

The main attention of present work is to study how benzeneacetamide interacts with other molecules in organic solvents. The frequencies of CO groups in 18 solvents were obtained by using infrared spectroscopy. The empirical parameters of the solvents as the acceptor number (AN), the van der Waals interaction parameters (S_VW) and the linear solvation energy relationships (LSER) were correlated with the frequencies of carbonyl stretching vibration (ν(CO)) of benzeneacetamide to estimate the contributions in intermolecular interactions. The results showed that solvent effects on the frequencies of CO stretching vibrations of benzeneacetamide were obvious. Self-association of alkanol leads to enhancement of O-H⋯O=C hydrogen bond strength and red-shift of the ν(CO) peak. The ν(CO) of benzeneacetamide is more vulnerable to the acidity of the hydrogen bond donor of the solvent. This research contributes to a thorough understanding of the molecular interactions and microstructures in the liquid mixtures.

Elucidation of Metal-Sugar Complexes: When Tungstate Combines with d-Mannose

The control of metal-sugar complexes speciation in solution is crucial in an energy transition context. Herein, the formation of tungstate-mannose complexes is unraveled in aqueous solution using a multitechnique experimental and theoretical approach. ¹³C nuclear magnetic resonance (NMR), as well as ¹³C-¹H and ¹H-¹H correlation spectra, analyzed in the light of coordination-induced shift method and conformation analysis, were employed to characterize the structure of the sugar involved in the complexes. X-ray absorption near edge structure spectroscopy was performed to provide relevant information about the metal electronic and coordination environment. The calculation of ¹³C NMR chemical shifts for a series of tungstate-mannose complexes using density functional theory (DFT) is a key to identify the appropriate structure among several candidates. Furthermore, a parametric study based on several relevant parameters, namely, pH and tungstate concentration, was carried out to look over the change of the nature and concentrations of the complexes. Two series of complexes were detected, in which the metallic core is either in a ditungstate or a monotungstate form. With respect to previous proposals, we identify two new species. Dinuclear complexes involve both α- and β-furanose forms chelating the metallic center in a tetradentate fashion. A hydrate form chelating a ditungstate core is also revealed. One monotungstate complex appears at high pH, in which a tetrahedral tungstate center is bound to α-mannofuranose through a monodentate site at the second deprotonated hydroxyl group. This unequalled level of knowledge opens the door to structure-reactivity relationships.

Intramolecular O···H Hydrogen Bonding of Salicylic Acid: Further Insights from O 1s XPS and 1H NMR Spectra Using DFT Calculations

Intramolecular hydrogen bonding (HB) is a complex phenomenon that extends beyond a simple valence event, affecting the core electrons of a molecule. Salicylic acid (SA) and its conformers provide an excellent model compound for studying intramolecular HB as the proton donor (H) and acceptor (O) can be toggled by rotating the C-O and C-C bonds to form up to seven potential conformers through various HB. In this study, we computationally investigated intramolecular interactions in SA conformers with and without such HB, by examining their calculated O 1s core electron-binding energy (CEBE) and ¹H NMR chemical shifts validated using recent measurements. The quantum mechanically stable SA conformers are fully defined by three rotatable bonds in the compound, which are abstracted as SA(η₁η₂η₃) digital structures, where η_i = 0 if the η_i angles match the most stable SA conformer (000) and η_i = 1 otherwise. Our findings suggest that the stability is dominated by the appearance of the intergroup intramolecular HB of H_p···O (where O is in the carboxylic acid functional group and H_p is the phenolic proton in -OH_p), and η₃ serves as a switch of such HB. As a result, the (η₁η₂0) SA conformers containing such H_p···O HB are more stable than other SA conformers (η₁η₂1) without such the H_p···O HB. The present density functional theory calculations reveal that this H_p···O HB results in splitting of the O 1s CEBEs of two hydroxyl groups (-OH) by up to 1 eV and deshielding the H_p proton ¹H NMR (δH_p) up to 11.68 ppm for the (η₁η₂0) conformers. Without such H_p···O HB, the O 1s XPS binding energies of two -OH groups will be closely located in the same band, and the ¹H NMR chemical shift of the H_p atom will be as small as an 4.09 ppm SA conformer [SA-G(101)]. The present study indicates that the O 1s CEBE splitting between two -OH groups serves as an indicator of the presence of the H_p···O HB in SA conformers, which is also supported by the ¹H NMR results.

London Dispersion Favors Sterically Hindered Diarylthiourea Conformers in Solution

We present an experimental and computational study on the conformers of N,N'-diphenylthiourea substituted with different dispersion energy donor (DED) groups. While the unfolded anti-anti conformer is the most relevant for thiourea catalysis, intramolecular noncovalent interactions counterintuitively favor the folded syn-syn conformer, as evident from a combination of low-temperature nuclear magnetic resonance measurements and computations. In order to quantify the noncovalent interactions, we utilized local energy decomposition analysis and symmetry-adapted perturbation theory at the DLPNO-CCSD(T)/def2-TZVPP and sSAPT0/6-311G(d,p) levels of theory. Additionally, we applied a double-mutant cycle to experimentally study the effects of bulky substituents on the equilibria. We determined London dispersion as the key interaction that shifts the equilibria towards the syn-syn conformers. This preference is likely a factor why such thiourea derivatives can be poor catalysts.

Azo-methoxy-calix[4]arene complexes with metal cations for chemical sensor applications: Characterization, QTAIM analyses and dispersion-corrected DFT- computations

In this work, the structures, quantum chemical descriptors, morphologic characterization of the azo-methoxy-calix[4]arene were investigated. The analyses and interpretation of the theoretical and the experimental IR spectroscopy results for the corresponding compounds was performed. The complexation of the azo-methoxy-calix[4]arene with Zn²⁺,Hg²⁺ , Cu²⁺ , Co²⁺, Ni²⁺ , Pb²⁺ and Cd²⁺metal cations has been calculated by the dispersion corrected density functional theory (DFT-D3). The values of the interaction energies show that the specific molecule is more selective to the Cu²⁺ cation. The study of the reactivity parameters confirms that the azo-methoxy-calix[4]arene molecule is more reactive and sensitive to the Cu²⁺ cation than that Co²⁺ and Cd²⁺. In addition, the investigation of the electrophilic and nucleophilic sites has been studied by the molecular electrostatic potential (MEP) analysis. The Hirshfeld surface (HS) analysis of the azo-methoxy-calix[4]arene-Cu²⁺ interaction have been used to understand the Cu⋯hydrogen-bond donors formed between the cation and the specific compound. The Quantum Theory of Atoms in Molecules (QTAIM) via Non covalent Interaction (NCI) analysis was carried out to demonstrate the nature, the type and the strength of the interaction formed between the Cu²⁺ cation and the two symmetrical ligands and the cavity. Finally, the chemical sensor properties based on the Si/SiO₂/Si₃N₄/Azo-methoxy-calix[4]arene for detection of Cu²⁺ cation were studied. Sensing performances are determined with a linear range from 10^-5.2 to 10^-2.2 M. The Si/SiO₂/Si₃N₄/azo-methoxy-calix[4]arene structure is a promoter to have a good performance sensor.

An Investigation of the Predominant Structure of Antibiotic Azithromycin in Chloroform Solution through NMR and Thermodynamic Analysis

Azithromycin (AZM) is a well-known macrolide-type antibiotic that has been used in the treatment of infections and inflammations. Knowledge of the predominant molecular structure in solution is a prerequisite for...

2-Chloro-4,6-bis{(E)-3-methoxy-4-[(4-methoxybenzyl)oxy]styryl}pyrimidine: Synthesis, Spectroscopic and Computational Evaluation

A novel curcumin analog namely 2-chloro-4,6-bis{(E)-3-methoxy-4-[(4-methoxybenzyl)oxy]-styryl}pyrimidine (compound 7) was synthesized by three-step reaction. The condensation reaction of protected vanillin with 2-chloro-4,6-dimethylpyrimidine (6) was the most efficient step, resulting in a total yield of 72%. The characterization of compound 7 was performed by 1H and 13C nuclear magnetic resonance (NMR), as well as high-resolution mass spectrometry. The experimental spectrometric data were compared with the theoretical spectra obtained by the density functional theory (DFT) method, showing a perfect match between them. UV-visible spectroscopy and steady-state fluorescence emission studies were performed for compound 7 in solvents of different polarities and the results were correlated with DFT calculations. Compound 7 showed a solvatochromism effect presenting higher molar extinction coefficient (log ε = 4.57) and fluorescence quantum yield (ϕ = 0.38) in toluene than in acetonitrile or methanol. The simulation of both frontier molecular orbitals (FMOs) and molecular electrostatic potential (MEP) suggested that the experimental spectra profile in toluene was not interfered by a possible charge transfer. These results are an indication of a low probability of compound 7 in reacting with unsaturated phospholipids in future applications as a fluorescent dye in biological systems.

Quantum Chemistry Calculations for Metabolomics

A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.

Unveiling the Molecular Structure of Antimalarial Drugs Chloroquine and Hydroxychloroquine in Solution through Analysis of 1H NMR Chemical Shifts

Chloroquine (CQ) and hydroxychloroquine (HCQ) have been standard antimalarial drugs since the early 1950s, and very recently, the possibility of their use for the treatment of COVID-19 patients has been considered. To understand the drug mode of action at the submicroscopic level (atoms and molecules), molecular modeling studies with the aid of computational chemistry methods have been of great help. A fundamental step in such theoretical investigations is the knowledge of the predominant drug molecular structure in solution, which is the real environment for the interaction with biological targets. Our strategy to access this valuable information is to perform density functional theory (DFT) calculations of ¹H NMR chemical shifts for several plausible molecular conformers and then find the best match with experimental NMR profile in solution (since it is extremely sensitive to conformational changes). Through this procedure, after optimizing 30 trial distinct molecular structures (ωB97x-D/6-31G(d,p)-PCM level of calculation), which may be considered representative conformations, we concluded that the global minimum (named M24), stabilized by an intramolecular N-H hydrogen bond, is not likely to be observed in water, chloroform, and dimethyl sulfoxide (DMSO) solution. Among fully optimized conformations (named M1 to M30, and MD1 and MD2), we found M12 (having no intramolecular H-bond) as the most probable structure of CQ and HCQ in water solution, which is a good approximate starting geometry in drug-receptor interaction simulations. On the other hand, the preferred CQ and HCQ structure in chloroform (and CQ in DMSO-d₆) solution was assigned as M8, showing the solvent effects on conformational preferences. We believe that the analysis of ¹H NMR data in solution can establish the connection between the macro level (experimental) and the sub-micro level (theoretical), which is not so apparent to us and appears to be more appropriate than the thermodynamic stability criterion in conformational analysis studies.

1H and 195Pt NMR prediction for inclusion compounds formed by cisplatin and oxidized carbon nanostructures

Prediction of NMR chemical shifts can assist experimentalists in the characterization of drug delivery systems based on carbon nanocomposites. Chemical shifts are strongly correlated to the nucleus position and its chemical neighborhood. Therefore, to predict structures and NMR properties of complex chemical models, choosing a more consistent theoretical level capable of providing more realistic results and moderate computational demand is a major challenge. In this work, we predicted the NMR spectra of inclusion compounds formed by cisplatin (cDDP) and an oxidized carbon nanotube (CNTox) and nanocone (CNCox) considered by specialists as potential drug delivery systems. The ¹⁹⁵Pt NMR chemical shifts calculated at the DFT level with the new relativistic NMR-DKH basis set were −2314 ppm and −2192 ppm for cDDP@CNTox and cDDP@CNCox complexes, respectively, which are both high-field shifted relative to the free cDDP (−2110 ppm). ¹H NMR chemical shifts are also sensitive to the inclusion process. The H (NH₃) signals are found on average at +4.3 (cDDP), −5.1 (cDDP@CNTox) and +6.6 ppm (cDDP@CNCox). Interestingly, despite the similar inclusion modes in CNTox and CNCox cavities, the ¹H NMR shifts were in opposite directions. A possible reason might be the higher stability of cDDP@CNTox (ΔE_F = −19.9 kcal mol⁻¹) than that of cDDP@CNCox (ΔE_F = −5.7 kcal mol⁻¹), which suggests a short guest–host contact in the former and consequently, a more efficient shielding of hydrogen atoms due to the electron-rich carbon structure. These results may be helpful as comparison data in the NMR spectra assignment in solution and the inclusion compounds' structural elucidation.

¹⁹⁵Pt NMR chemical shifts of the cisplatin molecule in the inclusion complex formed by oxidized carbon nanotubes.

Quantum chemical investigation of beta-CD–catechin flavonoid encapsulation in solution through NMR analysis: an adequate controlled drug-delivery system

DFT–PCM–water calculations of ¹H NMR chemical shifts for 28 optimized catechin–beta-CD complex structures revealed that adsorption mode of complexion should be predominant in aqueous media, with full-inclusion 1 : 1 structure being in total disagreement with experimental ¹H NMR profile (D₂O).

Accurate and cost-effective NMR chemical shift predictions for proteins using a molecules-in-molecules fragmentation-based method

We have developed an efficient protocol using our two-layer Molecules-in-Molecules (MIM2) fragmentation-based quantum chemical method for the prediction of NMR chemical shifts of large biomolecules. To investigate the performance of our fragmentation approach and demonstrate its applicability, MIM-NMR calculations are first calibrated on a test set of six proteins. The MIM2-NMR method yields a mean absolute deviation (MAD) from unfragmented full molecule calculations of 0.01 ppm for 1H and 0.06 ppm for 13C chemical shifts. Thus, the errors from fragmentation are only about 3% of our target accuracy of ∼0.3 ppm for 1H and 2-3 ppm for 13C chemical shifts. To compare with experimental chemical shifts, a standard protocol is first derived using two smaller proteins 2LHY (176 atoms) and 2LI1 (146 atoms) for obtaining an appropriate protein structure for NMR chemical shift calculations. The effect of the solvent environment on the calculated NMR chemical shifts is incorporated through implicit, explicit, or explicit-implicit solvation models. The expensive first solvation shell calculations are replaced by a micro-solvation model in which only the immediate interaction between the protein and the explicit solvation environment is considered. A single explicit water molecule for each amine and amide proton is found to be sufficient to yield accurate results for 1H chemical shifts. The 1H and 13C NMR chemical shifts calculated using our protocol give excellent agreement with experiments for two larger proteins, 2MC5 (the helical part with 265 atoms) and 3UMK (33 residue slice with 547 atoms). Overall, our target accuracy of ∼0.3 ppm for 1H and ∼2-3 ppm for 13C has been achieved for the larger proteins. The proposed MIM-NMR method is accurate and computationally cost-effective and should be applicable to study a wide range of large proteins.

Conformational Analysis of 5,4'-Dihydroxy-7,5',3'-trimethoxyisoflavone in Solution Using 1H NMR: A Density Functional Theory Approach

Among 20 compounds isolated from the extracts of Ouratea ferruginea the 5,4'-dihydroxy-7,5',3'-trimethoxyisoflavone (9) showed the best inhibitory effect on glutathione S-transferase (GST) and so deserves our attention. In this work we investigated the preferred molecular structure of 9 in chloroform solution using the density functional theory (DFT) and molecular dynamics simulation. Comparison between experimental ¹H NMR data in CDCl₃ solution and calculated chemical shifts enabled us to precisely determine the conformation adopted by 9 in solution, which can be used in further theoretical studies involving interaction with biological targets. Moreover, the experimental NMR data were used as reference to assess the ability of DFT based methods to predict ¹H NMR spectrum in solution for organic compounds. Among various DFT functionals the hybrid B3LYP was the most adequate for the calculation of chemical shifts in what CH_n protons are concerned. Regarding the OH hydrogen, inclusion of explicit CHCl₃ solvent molecules adequately placed around the solute led to good agreement with the experimental chemical shifts (in CDCl₃). It is a well-known fact that theoretical prediction of chemical shifts for OH hydrogens poses as a challenge and also revealed that the way the solvent effects are included in the DFT calculations is crucial for the right prediction of the whole ¹H NMR spectrum. It was found in this work that a supermolecule solute-solvent calculation with a minimum of four CHCl₃ molecules is enough to correctly reproduce the ¹H NMR experimental profile observed in solution, revealing that the calculated solvated structure used to reproduce the NMR chemical shifts is not unique.

Determination of Anticancer Zn(II)-Rutin Complex Structures in Solution through Density Functional Theory Calculations of 1H NMR and UV-VIS Spectra

Coordination compounds formed by flavonoid ligands are recognized as promising candidates as novel drugs with enhanced antioxidant and anticancer activity. Zn(II)-Rutin complexes have been described in the literature and distinct coordination modes proposed based on ¹H NMR/MS and IR/UV-VIS experimental spectroscopic data: 1:1/1:2 (Zn(II) binding to A-C rings) and 2:1 (Zn(II) binding to A-C-B rings) stoichiometry. Aiming to clarify these experimental findings and provide some physical insights into the process of complex formation in solution, we carried out density functional theory calculations of NMR and UV-VIS spectra for 25 plausible Zn(II)-Rutin molecular structures including solvent effect using the polarizable continuum model approach. The studied complexes in this work have 1:1, 1:2, 2:1, and 3:1 metal-ligand stoichiometry for all relevant Zn(II)-Rutin configurations. The least deviation between theoretical and experimental spectroscopic data was used as an initial criterion to select the probable candidate structures. Our theoretical spectroscopic results strongly indicate that the experimentally suggested modes of coordination (1:2 and 2:1) are likely to exist in solution, supporting the two distinct experimental findings in DMSO and methanol solution, which may be seen as an interesting result. Our predicted 1:2 and 2:1 metal complexes are in agreement with the experimental stoichiometry; however, they differ from the proposed structure. Besides the prediction of the coordination site and molecular structure in solution, an important contribution of this work is the determination of the OH-C5 deprotonation state of rutin due to metal complexation at the experimental conditions (pH = 6.7 and 7.20). We found that, in the two independent synthesis of metal complexes, distinct forms of rutin (OH-C5 and O^(-)-C5) are present, which are rather difficult to be assessed experimentally.

Structure of the flavonoid catechin in solution: NMR and quantum chemical investigations

DFT-PCM statistical index scan curves and ¹H-NMR profiles reveal conformational changes when a solid catechin sample is dissolved in acetone solvent.